%-12345X@PJL JOB @PJL SET STRINGCODESET=UTF8 @PJL SET HOLD=OFF @PJL SET RET=MEDIUM @PJL SET RESOLUTION=600 @PJL SET BITSPERPIXEL=2 @PJL SET ECONOMODE=OFF @PJL ENTER LANGUAGE=POSTSCRIPT %!PS-Adobe-3.0 %%Title: Microsoft Word - The SNP Classifier Manual.doc %%Creator: PScript5.dll Version 5.2.2 %%CreationDate: 12/7/2004 11:2:51 %%BoundingBox: (atend) %%Pages: (atend) %%Orientation: Portrait %%PageOrder: Special %%DocumentNeededResources: (atend) %%DocumentSuppliedResources: (atend) %%DocumentData: Clean7Bit %%TargetDevice: (HP LaserJet 4200) (3010.107) 0 %%LanguageLevel: 3 %%EndComments %%BeginDefaults %%PageBoundingBox: 12 12 599 779 %%ViewingOrientation: 1 0 0 1 %%EndDefaults %%BeginProlog %%BeginResource: file Pscript_WinNT_ErrorHandler 5.0 0 /currentpacking where{pop/oldpack currentpacking def/setpacking where{pop false setpacking}if}if/$brkpage 64 dict def $brkpage begin/prnt{dup type/stringtype ne{=string cvs}if dup length 6 mul/tx exch def/ty 10 def currentpoint/toy exch def/tox exch def 1 setgray newpath tox toy 2 sub moveto 0 ty rlineto tx 0 rlineto 0 ty neg rlineto closepath fill tox toy moveto 0 setgray show}bind def /nl{currentpoint exch pop lmargin exch moveto 0 -10 rmoveto}def/=={/cp 0 def typeprint nl}def/typeprint{dup type exec}readonly def/lmargin 72 def/rmargin 72 def/tprint{dup length cp add rmargin gt{nl/cp 0 def}if dup length cp add/cp exch def prnt}readonly def/cvsprint{=string cvs tprint( )tprint}readonly def /integertype{cvsprint}readonly def/realtype{cvsprint}readonly def/booleantype {cvsprint}readonly def/operatortype{(--)tprint =string cvs tprint(-- )tprint} readonly def/marktype{pop(-mark- )tprint}readonly def/dicttype{pop (-dictionary- )tprint}readonly def/nulltype{pop(-null- )tprint}readonly def /filetype{pop(-filestream- )tprint}readonly def/savetype{pop(-savelevel- ) tprint}readonly def/fonttype{pop(-fontid- )tprint}readonly def/nametype{dup xcheck not{(/)tprint}if cvsprint}readonly def/stringtype{dup rcheck{(\()tprint tprint(\))tprint}{pop(-string- )tprint}ifelse}readonly def/arraytype{dup rcheck {dup xcheck{({)tprint{typeprint}forall(})tprint}{([)tprint{typeprint}forall(]) tprint}ifelse}{pop(-array- )tprint}ifelse}readonly def/packedarraytype{dup rcheck{dup xcheck{({)tprint{typeprint}forall(})tprint}{([)tprint{typeprint} forall(])tprint}ifelse}{pop(-packedarray- )tprint}ifelse}readonly def/courier /Courier findfont 10 scalefont def end errordict/handleerror{systemdict begin $error begin $brkpage begin newerror{/newerror false store vmstatus pop pop 0 ne{grestoreall}if errorname(VMerror)ne{showpage}if initgraphics courier setfont lmargin 720 moveto errorname(VMerror)eq{userdict/ehsave known{clear userdict /ehsave get restore 2 vmreclaim}if vmstatus exch pop exch pop PrtVMMsg}{ (ERROR: )prnt errorname prnt nl(OFFENDING COMMAND: )prnt/command load prnt $error/ostack known{nl nl(STACK:)prnt nl nl $error/ostack get aload length{==} repeat}if}ifelse systemdict/showpage get exec(%%[ Error: )print errorname =print(; OffendingCommand: )print/command load =print( ]%%)= flush}if end end end}dup 0 systemdict put dup 4 $brkpage put bind readonly put/currentpacking where{pop/setpacking where{pop oldpack setpacking}if}if %%EndResource userdict /Pscript_WinNT_Incr 230 dict dup begin put %%BeginResource: file Pscript_FatalError 5.0 0 userdict begin/FatalErrorIf{{initgraphics findfont 1 index 0 eq{exch pop}{dup length dict begin{1 index/FID ne{def}{pop pop}ifelse}forall/Encoding {ISOLatin1Encoding}stopped{StandardEncoding}if def currentdict end /ErrFont-Latin1 exch definefont}ifelse exch scalefont setfont counttomark 3 div cvi{moveto show}repeat showpage quit}{cleartomark}ifelse}bind def end %%EndResource userdict begin/PrtVMMsg{vmstatus exch sub exch pop gt{[ (This job requires more memory than is available in this printer.)100 500 (Try one or more of the following, and then print again:)100 485 (For the output format, choose Optimize For Portability.)115 470 (In the Device Settings page, make sure the Available PostScript Memory is accurate.) 115 455(Reduce the number of fonts in the document.)115 440 (Print the document in parts.)115 425 12/Times-Roman showpage (%%[ PrinterError: Low Printer VM ]%%)= true FatalErrorIf}if}bind def end version cvi 2016 ge{/VM?{pop}bind def}{/VM? userdict/PrtVMMsg get def}ifelse 105000 VM? %%BeginResource: file Pscript_Win_Basic 5.0 0 /d/def load def/,/load load d/~/exch , d/?/ifelse , d/!/pop , d/`/begin , d/^ /index , d/@/dup , d/+/translate , d/$/roll , d/U/userdict , d/M/moveto , d/- /rlineto , d/&/currentdict , d/:/gsave , d/;/grestore , d/F/false , d/T/true , d/N/newpath , d/E/end , d/Ac/arc , d/An/arcn , d/A/ashow , d/D/awidthshow , d/C /closepath , d/V/div , d/O/eofill , d/L/fill , d/I/lineto , d/-c/curveto , d/-M /rmoveto , d/+S/scale , d/Ji/setfont , d/Lc/setlinecap , d/Lj/setlinejoin , d /Lw/setlinewidth , d/Lm/setmiterlimit , d/sd/setdash , d/S/show , d/LH/showpage , d/K/stroke , d/W/widthshow , d/R/rotate , d/L2? false/languagelevel where{pop languagelevel 2 ge{pop true}if}if d L2?{/xS/xshow , d/yS/yshow , d/zS/xyshow , d}if/b{bind d}bind d/bd{bind d}bind d/xd{~ d}bd/ld{, d}bd/bn/bind ld/lw/Lw ld /lc/Lc ld/lj/Lj ld/sg/setgray ld/ADO_mxRot null d/self & d/OrgMx matrix currentmatrix d/reinitialize{: OrgMx setmatrix[/TextInit/GraphInit/UtilsInit counttomark{@ where{self eq}{F}?{cvx exec}{!}?}repeat cleartomark ;}b /initialize{`{/Pscript_Win_Data where{!}{U/Pscript_Win_Data & put}?/ADO_mxRot ~ d/TextInitialised? 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F d reinitialize}?}b/terminate{!{& self eq {exit}{E}?}loop E}b/suspend/terminate , d/resume{` Pscript_Win_Data `}b U ` /lucas 21690 d/featurebegin{countdictstack lucas[}b/featurecleanup{stopped {cleartomark @ lucas eq{! exit}if}loop countdictstack ~ sub @ 0 gt{{E}repeat} {!}?}b E/snap{transform 0.25 sub round 0.25 add ~ 0.25 sub round 0.25 add ~ itransform}b/dsnap{dtransform round ~ round ~ idtransform}b/nonzero_round{@ 0.5 ge{round}{@ -0.5 lt{round}{0 ge{1}{-1}?}?}?}b/nonzero_dsnap{dtransform nonzero_round ~ nonzero_round ~ idtransform}b U<04>cvn{}put/rr{1 ^ 0 - 0 ~ - neg 0 - C}b/irp{4 -2 $ + +S fx 4 2 $ M 1 ^ 0 - 0 ~ - neg 0 -}b/rp{4 2 $ M 1 ^ 0 - 0 ~ - neg 0 -}b/solid{[]0 sd}b/g{@ not{U/DefIf_save save put}if U/DefIf_bool 2 ^ put}b/DefIf_El{if U/DefIf_bool get not @{U/DefIf_save get restore}if}b/e {DefIf_El !}b/UDF{L2?{undefinefont}{!}?}b/UDR{L2?{undefineresource}{! !}?}b /freeVM{/Courier findfont[40 0 0 -40 0 0]makefont Ji 2 vmreclaim}b/hfRedefFont {findfont @ length dict `{1 ^/FID ne{d}{! !}?}forall & E @ ` ~{/CharStrings 1 dict `/.notdef 0 d & E d}if/Encoding 256 array 0 1 255{1 ^ ~/.notdef put}for d E definefont !}bind d/hfMkCIDFont{/CIDFont findresource @ length 2 add dict `{1 ^ @/FID eq ~ @/XUID eq ~/UIDBase eq or or{! !}{d}?}forall/CDevProc ~ d/Metrics2 16 dict d/CIDFontName 1 ^ d & E 1 ^ ~/CIDFont defineresource ![~]composefont !} bind d %%EndResource %%BeginResource: file Pscript_Win_Utils_L2 5.0 0 /rf/rectfill , d/fx{1 1 dtransform @ 0 ge{1 sub 0.5}{1 add -0.5}? 3 -1 $ @ 0 ge {1 sub 0.5}{1 add -0.5}? 3 1 $ 4 1 $ idtransform 4 -2 $ idtransform}b/BZ{4 -2 $ snap + +S fx rf}b/rs/rectstroke , d/rc/rectclip , d/UtilsInit{currentglobal{F setglobal}if}b/scol{! setcolor}b/colspA/DeviceGray d/colspABC/DeviceRGB d /colspRefresh{colspABC setcolorspace}b/SetColSpace{colspABC setcolorspace}b /resourcestatus where{!/ColorRendering/ProcSet resourcestatus{! ! T}{F}?}{F}? not{/ColorRendering<>/defineresource where{!/ProcSet defineresource !}{! !}?}if/buildcrdname{/ColorRendering/ProcSet findresource ` mark GetHalftoneName @ type @/nametype ne ~/stringtype ne and{!/none}if(.) GetPageDeviceName @ type @/nametype ne ~/stringtype ne and{!/none}if(.)5 ^ 0 5 -1 1{^ length add}for string 6 1 $ 5 ^ 5{~ 1 ^ cvs length 1 ^ length 1 ^ sub getinterval}repeat ! cvn 3 1 $ ! ! E}b/definecolorrendering{~ buildcrdname ~ /ColorRendering defineresource !}b/findcolorrendering where{!}{ /findcolorrendering{buildcrdname @/ColorRendering resourcestatus{! ! T}{ /ColorRendering/ProcSet findresource ` GetSubstituteCRD E F}?}b}? /selectcolorrendering{findcolorrendering !/ColorRendering findresource setcolorrendering}b/G2UBegin{findresource/FontInfo get/GlyphNames2Unicode get `}bind d/G2CCBegin{findresource/FontInfo get/GlyphNames2HostCode get `}bind d /G2UEnd{E}bind d/AddFontInfoBegin{/FontInfo 8 dict @ `}bind d/AddFontInfo{ /GlyphNames2Unicode 16 dict d/GlyphNames2HostCode 16 dict d}bind d /AddFontInfoEnd{E d}bind d/T0AddCFFMtx2{/CIDFont findresource/Metrics2 get ` d E}bind d %%EndResource end %%EndProlog %%BeginSetup currentpagedevice /MediaProcessing known {<> >> setpagedevice}{<< /StapleDetails<< /Type 8 /Portrait true>> >> setpagedevice} ifelse statusdict begin (%%[ ProductName: ) print product print ( ]%%)= flush end [ 1 0 0 1 0 0 ] false Pscript_WinNT_Incr dup /initialize get exec featurebegin{ %%BeginNonPPDFeature: JobTimeout 0 0 /languagelevel where{pop languagelevel}{1}ifelse 2 ge{1 dict dup/JobTimeout 4 -1 roll put setuserparams}{statusdict/setjobtimeout get exec}ifelse %%EndNonPPDFeature }featurecleanup featurebegin{ %%BeginNonPPDFeature: WaitTimeout 120 120 /languagelevel where{pop languagelevel}{1}ifelse 2 ge{1 dict dup/WaitTimeout 4 -1 roll put setuserparams}{statusdict/waittimeout 3 -1 roll put}ifelse %%EndNonPPDFeature }featurecleanup featurebegin{ %%BeginFeature: *Collate True <> setpagedevice %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *PageSize Letter <> setpagedevice %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *StapleLocation None << /MediaProcessing (NONE) >> >> setpagedevice %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *OutputBin Auto %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *MediaType Auto %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *Duplex DuplexNoTumble <> setpagedevice %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *HPXMLFileUsed HPXMLFileName %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *HPColorMode MONOCHROME_MODE %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *PrintQualityGroup PQGroup_2 %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *HPOrientRotate180 False %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *TextAsBlack False %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *JRConstraints JRCHDPartial %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *JRHDInstalled JRHDOff %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *JRHDNotInstalled JRHDOff %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *HPJobAccounting HPJOBACCT_JOBACNT %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *EnvFeeder NotInstalled %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *Tray3 Tray3_500 %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *Tray4 NotInstalled %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *AccessoryOutputBins None %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *DuplexUnit Installed %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *InstalledMemory 64-79MB %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *PrinterHardDisk NotInstalled %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *JobRetention Installed %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *DeviceIsMopier Installed %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *HPInstallableTrayFeatureName EnvFeeder %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *HPInstallableTraySize EnvFeeder-100-ENVELOPE_FEEDER %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *HPInstallableHCO 500Stacker-Q2442 %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *ActualCustomRange 215900_355600 %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *HPPDLType PDL_PS %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *HPPJLEncoding UTF8 %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *ScaleFromLargePaper Installed %%EndFeature }featurecleanup featurebegin{ %%BeginFeature: *CombineMediaTypesAndInputBins Installed %%EndFeature }featurecleanup 1 setlinecap 1 setlinejoin /mysetup [ 72 600 V 0 0 -72 600 V 11.99905 779.0003 ] def %%EndSetup userdict begin /ehsave save def end %%Page: 1 1 %%PageBoundingBox: 12 12 599 779 %%EndPageComments %%BeginPageSetup /DeviceRGB dup setcolorspace /colspABC exch def mysetup concat colspRefresh %%EndPageSetup /DeviceGray dup setcolorspace /colspABC exch def 0 0 scol Pscript_WinNT_Incr begin %%BeginResource: file Pscript_Text 5.0 0 /TextInit{TextInitialised? not{/Pscript_Windows_Font & d/TextInitialised? T d /fM[1 0 0 1 0 0]d/mFM matrix d/iMat[1 0 0.212557 1 0 0]d}if}b/copyfont{1 ^ length add dict `{1 ^/FID ne{d}{! !}?}forall & E}b/EncodeDict 11 dict d/bullets {{/bullet}repeat}b/rF{3 copyfont @ ` ~ EncodeDict ~ get/Encoding ~ 3 ^/0 eq{& /CharStrings known{CharStrings/Eth known not{! EncodeDict/ANSIEncodingOld get} if}if}if d E}b/mF{@ 7 1 $ findfont ~{@/Encoding get @ StandardEncoding eq{! T}{ {ISOLatin1Encoding}stopped{! F}{eq}?{T}{@ ` T 32 1 127{Encoding 1 ^ get StandardEncoding 3 -1 $ get eq and}for E}?}?}{F}?{1 ^ ~ rF}{0 copyfont}? 6 -2 $ ! ! ~ !/pd_charset @ where{~ get 128 eq{@ FDV 2 copy get @ length array copy put pd_CoverFCRange}if}{!}? 2 ^ ~ definefont fM 5 4 -1 $ put fM 4 0 put fM makefont Pscript_Windows_Font 3 1 $ put}b/sLT{: Lw -M currentpoint snap M 0 - 0 Lc K ;}b/xUP null d/yUP null d/uW null d/xSP null d/ySP null d/sW null d/sSU{N /uW ~ d/yUP ~ d/xUP ~ d}b/sU{xUP yUP uW sLT}b/sST{N/sW ~ d/ySP ~ d/xSP ~ d}b/sT {xSP ySP sW sLT}b/sR{: + R 0 0 M}b/sRxy{: matrix astore concat 0 0 M}b/eR/; , d /AddOrigFP{{&/FontInfo known{&/FontInfo get length 6 add}{6}? dict ` /WinPitchAndFamily ~ d/WinCharSet ~ d/OrigFontType ~ d/OrigFontStyle ~ d /OrigFontName ~ d & E/FontInfo ~ d}{! ! ! ! !}?}b/mFS{makefont Pscript_Windows_Font 3 1 $ put}b/mF42D{0 copyfont `/FontName ~ d 2 copy ~ sub 1 add dict `/.notdef 0 d 2 copy 1 ~{@ 3 ^ sub Encoding ~ get ~ d}for & E /CharStrings ~ d ! ! & @ E/FontName get ~ definefont}b/mF42{15 dict ` @ 4 1 $ FontName ~ d/FontType 0 d/FMapType 2 d/FontMatrix[1 0 0 1 0 0]d 1 ^ 254 add 255 idiv @ array/Encoding ~ d 0 1 3 -1 $ 1 sub{@ Encoding 3 1 $ put}for/FDepVector Encoding length array d/CharStrings 2 dict `/.notdef 0 d & E d 0 1 Encoding length 1 sub{@ @ 10 lt{! FontName length 1 add string}{100 lt{FontName length 2 add string}{FontName length 3 add string}?}? @ 0 FontName @ length string cvs putinterval @ 3 -1 $ @ 4 1 $ 3 string cvs FontName length ~ putinterval cvn 1 ^ 256 mul @ 255 add 3 -1 $ 4 ^ findfont mF42D FDepVector 3 1 $ put}for & @ E /FontName get ~ definefont ! ! ! mF}b/mF_OTF_V{~ ! ~ ! 4 -1 $ ! findfont 2 ^ ~ definefont fM @ @ 4 6 -1 $ neg put 5 0 put 90 matrix R matrix concatmatrix makefont Pscript_Windows_Font 3 1 $ put}b/mF_TTF_V{3{~ !}repeat 3 -1 $ ! findfont 1 ^ ~ definefont Pscript_Windows_Font 3 1 $ put}b/UmF{L2? {Pscript_Windows_Font ~ undef}{!}?}b/UmF42{@ findfont/FDepVector get{/FontName get undefinefont}forall undefinefont}b %%EndResource end reinitialize Pscript_WinNT_Incr begin %%BeginResource: file Pscript_Encoding256 5.0 0 /CharCol256Encoding[/.notdef/breve/caron/dotaccent/dotlessi/fi/fl/fraction /hungarumlaut/Lslash/lslash/minus/ogonek/ring/Zcaron/zcaron/.notdef/.notdef /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef /.notdef/.notdef/.notdef/.notdef/.notdef/space/exclam/quotedbl/numbersign /dollar/percent/ampersand/quotesingle/parenleft/parenright/asterisk/plus/comma /hyphen/period/slash/zero/one/two/three/four/five/six/seven/eight/nine/colon /semicolon/less/equal/greater/question/at/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S /T/U/V/W/X/Y/Z/bracketleft/backslash/bracketright/asciicircum/underscore/grave /a/b/c/d/e/f/g/h/i/j/k/l/m/n/o/p/q/r/s/t/u/v/w/x/y/z/braceleft/bar/braceright /asciitilde/.notdef/Euro/.notdef/quotesinglbase/florin/quotedblbase/ellipsis /dagger/daggerdbl/circumflex/perthousand/Scaron/guilsinglleft/OE/.notdef /.notdef/.notdef/.notdef/quoteleft/quoteright/quotedblleft/quotedblright/bullet /endash/emdash/tilde/trademark/scaron/guilsinglright/oe/.notdef/.notdef /Ydieresis/.notdef/exclamdown/cent/sterling/currency/yen/brokenbar/section /dieresis/copyright/ordfeminine/guillemotleft/logicalnot/.notdef/registered /macron/degree/plusminus/twosuperior/threesuperior/acute/mu/paragraph /periodcentered/cedilla/onesuperior/ordmasculine/guillemotright/onequarter /onehalf/threequarters/questiondown/Agrave/Aacute/Acircumflex/Atilde/Adieresis /Aring/AE/Ccedilla/Egrave/Eacute/Ecircumflex/Edieresis/Igrave/Iacute /Icircumflex/Idieresis/Eth/Ntilde/Ograve/Oacute/Ocircumflex/Otilde/Odieresis /multiply/Oslash/Ugrave/Uacute/Ucircumflex/Udieresis/Yacute/Thorn/germandbls /agrave/aacute/acircumflex/atilde/adieresis/aring/ae/ccedilla/egrave/eacute /ecircumflex/edieresis/igrave/iacute/icircumflex/idieresis/eth/ntilde/ograve /oacute/ocircumflex/otilde/odieresis/divide/oslash/ugrave/uacute/ucircumflex /udieresis/yacute/thorn/ydieresis]def EncodeDict/256 CharCol256Encoding put %%EndResource end reinitialize %%IncludeResource: font Garamond-Halbfett Pscript_WinNT_Incr begin %%BeginResource: file Pscript_Win_Euro_L2 5.0 0 /UseT3EuroFont{/currentdistillerparams where{pop currentdistillerparams /CoreDistVersion get 4000 le}{false}ifelse}bind def/NewEuroT3Font?{dup/FontType get 3 eq{dup/EuroFont known exch/BaseFont known and}{pop false}ifelse}bind def /T1FontHasEuro{dup/CharStrings known not{dup NewEuroT3Font?{dup/EuroGlyphName get exch/EuroFont get/CharStrings get exch known{true}{false}ifelse}{pop false} ifelse}{dup/FontType get 1 eq{/CharStrings get/Euro known}{dup/InfoDict known{ /InfoDict get/Euro known}{/CharStrings get/Euro known}ifelse}ifelse}ifelse}bind def/FontHasEuro{findfont dup/Blend known{pop true}{T1FontHasEuro}ifelse}bind def/EuroEncodingIdx 1 def/EuroFontHdr{12 dict begin/FontInfo 10 dict dup begin /version(001.000)readonly def/Notice(Copyright (c)1999 Adobe Systems Incorporated. All Rights Reserved.)readonly def/FullName(Euro)readonly def /FamilyName(Euro)readonly def/Weight(Regular)readonly def/isFixedPitch false def/ItalicAngle 0 def/UnderlinePosition -100 def/UnderlineThickness 50 def end readonly def/FontName/Euro def/Encoding 256 array 0 1 255{1 index exch/.notdef put}for def/PaintType 0 def/FontType 1 def/FontMatrix[0.001 0 0 0.001 0 0]def /FontBBox{-25 -23 1500 804}readonly def currentdict end dup/Private 20 dict dup begin/ND{def}def/NP{put}def/lenIV -1 def/RD{string currentfile exch readhexstring pop}def/-|{string currentfile exch readstring pop}executeonly def /|-{def}executeonly def/|{put}executeonly def/BlueValues[-20 0 706 736 547 572] |-/OtherBlues[-211 -203]|-/BlueScale 0.0312917 def/MinFeature{16 16}|-/StdHW [60]|-/StdVW[71]|-/ForceBold false def/password 5839 def/Erode{8.5 dup 3 -1 roll 0.1 mul exch 0.5 sub mul cvi sub dup mul 71 0 dtransform dup mul exch dup mul add le{pop pop 1.0 1.0}{pop pop 0.0 1.5}ifelse}def/OtherSubrs[{}{}{} {systemdict/internaldict known not{pop 3}{1183615869 systemdict/internaldict get exec dup/startlock known{/startlock get exec}{dup/strtlck known{/strtlck get exec}{pop 3}ifelse}ifelse}ifelse}executeonly]|-/Subrs 5 array dup 0 <8E8B0C100C110C110C210B>put dup 1<8B8C0C100B>put dup 2<8B8D0C100B>put dup 3<0B> put dup 4<8E8C8E0C100C110A0B>put |- 2 index/CharStrings 256 dict dup begin /.notdef<8b8b0d0e>def end end put put dup/FontName get exch definefont pop}bind def/AddEuroGlyph{2 index exch EuroEncodingIdx 1 eq{EuroFontHdr}if systemdict begin/Euro findfont dup dup/Encoding get 5 1 roll/Private get begin/CharStrings get dup 3 index known{pop pop pop pop end end}{begin 1 index exch def end end end EuroEncodingIdx dup 1 add/EuroEncodingIdx exch def exch put}ifelse}bind def /GetNewXUID{currentdict/XUID known{[7 XUID aload pop]true}{currentdict/UniqueID known{[7 UniqueID]true}{false}ifelse}ifelse}bind def/BuildT3EuroFont{exch 16 dict begin dup/FontName exch def findfont dup/Encoding get/Encoding exch def dup length 1 add dict copy dup/FID undef begin dup dup/FontName exch def /Encoding 256 array 0 1 255{1 index exch/.notdef put}for def GetNewXUID{/XUID exch def}if currentdict end definefont pop/BaseFont exch findfont 1000 scalefont def/EuroFont exch findfont 1000 scalefont def pop/EuroGlyphName exch def/FontType 3 def/FontMatrix[.001 0 0 .001 0 0]def/FontBBox BaseFont/FontBBox get def/Char 1 string def/BuildChar{exch dup begin/Encoding get 1 index get /Euro eq{BaseFont T1FontHasEuro{false}{true}ifelse}{false}ifelse{EuroFont setfont pop userdict/Idx 0 put EuroFont/Encoding get{EuroGlyphName eq{exit} {userdict/Idx Idx 1 add put}ifelse}forall userdict/Idx get}{dup dup Encoding exch get BaseFont/Encoding get 3 1 roll put BaseFont setfont}ifelse Char 0 3 -1 roll put Char stringwidth newpath 0 0 moveto Char true charpath flattenpath pathbbox setcachedevice 0 0 moveto Char show end}bind def currentdict end dup /FontName get exch definefont pop}bind def/AddEuroToT1Font{dup findfont dup length 10 add dict copy dup/FID undef begin/EuroFont 3 -1 roll findfont 1000 scalefont def CharStrings dup length 1 add dict copy begin/Euro{EuroFont setfont pop EuroGBBox aload pop setcachedevice 0 0 moveto EuroGName glyphshow} bind def currentdict end/CharStrings exch def GetNewXUID{/XUID exch def}if 3 1 roll/EuroGBBox exch def/EuroGName exch def currentdict end definefont pop}bind def/BuildNewFont{UseT3EuroFont{BuildT3EuroFont}{pop AddEuroToT1Font}ifelse}bind def/UseObliqueEuro{findfont/FontMatrix get dup 2 get 0 eq exch dup 0 get exch 3 get eq and UseT3EuroFont or}bind def %%EndResource end reinitialize 7500 VM? /Garamond-Halbfett FontHasEuro not { /Euro.Garamond-Halbfett [500 0 19 -13 492 688 ] <9EF8880DF84CA6037EA701F791C801F7FFC801F928A7018F0AC3F73203F852A6037EA701 F791C801F7FFC801F928A701F86DF89C15F73A0770068875877D778B08858B749A799308 7E916E946B8B08358BFB144773FB58086506774E05C1065A076706774E05C7069DFB27E1 FB0BF7188B088F0AC3F73203F84CA6037EA701F791C801F7FFC801F928A701B88BAA9F91 8E089C939892908B089F8B8F7D8E7508A606F7450772067A3F5240538B084F8B68EC89F7 2108F72F06A0C805FB4506BC07F75506A0C805FB690690F71CA9EFC88B088F0AF852A603 7EA701F791C801F7FFC801F928A701D58BB93A9C5008090E> AddEuroGlyph /Euro /Garamond-Halbfett /Garamond-Halbfett-Copy BuildNewFont } if F /F0 0 /256 T /Garamond-Halbfett mF /F0S96 F0 [150 0 0 -150 0 0 ] mFS F0S96 Ji 650 621 M (The SNP Classifier Manual)[103 83 70 38 77 127 92 37 102 39 72 62 62 42 45 42 70 52 38 137 72 83 83 72 0]xS 2389 621 M ( )S %%IncludeResource: font Garamond-Antiqua 7500 VM? /Garamond-Antiqua FontHasEuro not { /Euro.Garamond-Antiqua [500 0 24 -14 493 676 ] AddEuroGlyph /Euro /Garamond-Antiqua /Garamond-Antiqua-Copy BuildNewFont } if F /F1 0 /256 T /Garamond-Antiqua mF /F1S64 F1 [100 0 0 -100 0 0 ] mFS F1S64 Ji 650 747 M (Written By Kelvin Li)[89 33 23 29 29 42 51 25 61 42 25 74 42 23 47 23 51 25 57 0]xS 1464 747 M ( )S 650 859 M (J. Craig Venter Institute)[33 22 25 64 33 41 23 45 25 68 42 51 29 42 33 25 35 51 36 29 23 29 49 29 0]xS 1574 859 M ( )S 650 972 M ( )S 650 1084 M (Version 0.00)[68 42 33 36 23 51 51 25 47 22 47 0]xS 1142 1084 M ( )S LH (%%[Page: 1]%%) = %%PageTrailer %%Page: 2 2 %%PageBoundingBox: 12 12 599 779 %%EndPageComments %%BeginPageSetup /DeviceRGB dup setcolorspace /colspABC exch def mysetup concat colspRefresh %%EndPageSetup /DeviceGray dup setcolorspace /colspABC exch def 0 0 scol F0S96 Ji 650 621 M (Table of Contents)[103 72 83 39 70 38 78 45 38 102 78 83 47 69 83 47 0]xS 1787 621 M ( )S F1S64 Ji 650 797 M (Introduction)[35 51 29 33 51 50 49 42 29 23 51 0]xS 1166 797 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 1870 797 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2574 797 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3278 797 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3982 797 M (.........)[22 22 22 22 22 22 22 22 0]xS 4199 797 M (3)S %%IncludeResource: font TimesNewRoman 7500 VM? /TimesNewRoman FontHasEuro not { /Euro.TimesNewRoman [500 0 24 -14 493 676 ] AddEuroGlyph /Euro /TimesNewRoman /TimesNewRoman-Copy BuildNewFont } if F /F2 0 /256 T /TimesNewRoman mF /F2S64 F2 [100 0 0 -100 0 0 ] mFS F2S64 Ji 4246 797 M ( )S F1S64 Ji 650 909 M (SNP Classification)[48 77 56 25 64 23 41 36 36 23 32 23 42 41 29 23 51 0]xS 1386 909 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2090 909 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2794 909 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3498 909 M (...............................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 909 M (3)S F2S64 Ji 4246 909 M ( )S F1S64 Ji 750 1022 M (Algorithm Overview)[68 23 45 51 33 23 29 51 77 25 78 47 42 33 47 23 42 0]xS 1562 1022 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2266 1022 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2970 1022 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3674 1022 M (.......................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 1022 M (3)S F2S64 Ji 4246 1022 M ( )S F1S64 Ji 750 1134 M (Extracting Coding Information)[66 46 29 33 41 42 29 23 51 45 25 64 51 50 23 50 45 25 35 51 32 51 33 78 41 29 23 51 0]xS 1980 1134 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2684 1134 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3388 1134 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4092 1134 M (....)[22 22 22 0]xS 4199 1134 M (4)S F2S64 Ji 4246 1134 M ( )S F1S64 Ji 850 1247 M (Single)[48 23 51 45 23 0]xS 1082 1247 M ( Region Extraction)[25 62 42 45 23 51 51 25 66 46 29 33 40 42 29 23 51 0]xS 1826 1247 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2530 1247 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3234 1247 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3938 1247 M (...........)[22 22 22 22 22 22 22 22 22 22 0]xS 4199 1247 M (5)S F2S64 Ji 4246 1247 M ( )S %%IncludeResource: font Garamond-Kursiv 7500 VM? /Garamond-Kursiv FontHasEuro not { /Euro.Garamond-Kursiv [500 0 23 -7 578 676 ] AddEuroGlyph /Euro /Garamond-Kursiv /Garamond-Kursiv-Copy BuildNewFont } if F /F3 0 /256 T /Garamond-Kursiv mF /F3S64 F3 [100 0 0 -100 0 0 ] mFS F3S64 Ji 850 1359 M (Batched Regions Extraction)[56 41 25 27 42 29 41 25 63 29 32 23 35 43 29 25 69 50 25 30 41 27 25 23 35 0]xS F1S64 Ji 1782 1359 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2486 1359 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3190 1359 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3894 1359 M (.............)[22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 1359 M (5)S F2S64 Ji 4246 1359 M ( )S F1S64 Ji 750 1472 M (Classifying SNPs)[64 23 41 36 36 23 32 42 23 51 45 25 48 77 56 0]xS 1408 1472 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2112 1472 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2816 1472 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3520 1472 M (..............................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 1472 M (6)S F2S64 Ji 4246 1472 M ( )S F1S64 Ji 850 1584 M (Alleles Input File)[68 23 23 42 23 42 36 25 35 51 51 49 29 25 56 23 23 0]xS 1518 1584 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2222 1584 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2926 1584 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3630 1584 M (.........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 1584 M (6)S F2S64 Ji 4246 1584 M ( )S F1S64 Ji 850 1697 M (Running the SNP Classifier)[63 49 51 51 23 51 45 25 29 51 42 25 48 77 56 25 64 22 41 36 36 23 32 23 42 0]xS 1914 1697 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2618 1697 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3322 1697 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4026 1697 M (.......)[22 22 22 22 22 22 0]xS 4199 1697 M (7)S F2S64 Ji 4246 1697 M ( )S F1S64 Ji 950 1809 M (Classifying SNPs by Template)[64 23 41 36 36 23 32 42 23 51 45 25 48 77 56 36 25 51 42 25 61 42 77 51 23 41 29 0]xS 2134 1809 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2838 1809 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3542 1809 M (.............................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 1809 M (7)S F2S64 Ji 4246 1809 M ( )S F3S64 Ji 950 1922 M (Mapping Amplicons to )[82 41 41 41 23 43 32 25 76 62 41 22 23 27 35 43 29 25 25 35 0]xS 1746 1922 M (Extracted Coding Information Coordinates)[69 50 25 30 40 27 25 29 41 25 63 35 41 23 43 32 25 32 43 22 35 30 63 41 25 23 35 43 25 63 35 35 30 41 23 43 41 25 29 0]xS F1S64 Ji 3190 1922 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3894 1922 M (.............)[22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 1922 M (7)S F2S64 Ji 4246 1922 M ( )S F3S64 Ji 950 2034 M (Classifying SNP)[63 22 41 29 29 23 22 33 23 43 32 25 50 78 0]xS 1516 2034 M (s)S 1545 2034 M ( by Batch)[25 41 33 25 56 41 25 27 0]xS F1S64 Ji 1870 2034 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2574 2034 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3278 2034 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3982 2034 M (.........)[22 22 22 22 22 22 22 22 0]xS 4199 2034 M (7)S F2S64 Ji 4246 2034 M ( )S F1S64 Ji 850 2147 M (QC\222ing SNP Classification)[77 64 22 23 51 45 25 48 77 56 25 64 23 41 36 36 23 32 23 42 41 29 23 50 0]xS 1892 2147 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2596 2147 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3300 2147 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4004 2147 M (........)[22 22 22 22 22 22 22 0]xS 4199 2147 M (8)S F2S64 Ji 4246 2147 M ( )S F1S64 Ji 950 2259 M (C)S 1014 2259 M (hecking the Flanking Sequence)[51 42 42 47 23 50 45 25 29 51 42 25 56 23 41 51 47 23 51 45 25 47 41 49 49 42 51 42 0]xS 2222 2259 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2926 2259 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3630 2259 M (.........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 2259 M (8)S F2S64 Ji 4246 2259 M ( )S F1S64 Ji 950 2372 M (Verification through a dbSNP Proxy)[68 42 33 23 32 23 42 41 29 23 51 51 25 29 51 33 51 49 45 51 25 41 25 50 50 48 77 56 25 56 33 51 46 0]xS 2376 2372 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3080 2372 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3784 2372 M (..................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 2372 M (8)S F2S64 Ji 4246 2372 M ( )S F1S64 Ji 750 2484 M (Allele Frequencies)[68 23 23 42 23 42 25 56 33 42 49 49 42 50 42 23 42 0]xS 1474 2484 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2178 2484 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2882 2484 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3586 2484 M (...........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 2484 M (9)S F2S64 Ji 4246 2484 M ( )S F1S64 Ji 850 2597 M (Computing Frequencies of Variations)[64 51 77 51 49 29 23 51 45 25 56 33 42 49 49 42 51 42 23 42 36 25 50 32 25 68 41 33 23 41 29 23 51 51 0]xS 2310 2597 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3014 2597 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3718 2597 M (.....................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4199 2597 M (9)S F2S64 Ji 4246 2597 M ( )S F3S64 Ji 850 2709 M (Computing Allele Frequencies by Batch)[63 35 63 41 43 25 22 43 32 25 76 22 22 29 22 29 25 57 30 29 43 43 29 43 27 23 29 29 25 41 33 25 56 41 25 27 0]xS F1S64 Ji 2178 2709 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2882 2709 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3586 2709 M (.........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 2709 M (10)[47 0]xS F2S64 Ji 4246 2709 M ( )S F1S64 Ji 850 2822 M (File Formatting Tools)[56 23 23 42 25 56 51 33 77 41 29 29 23 51 45 25 61 51 51 23 0]xS 1716 2822 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2420 2822 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3124 2822 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3828 2822 M (..............)[22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 2822 M (10)[47 0]xS F2S64 Ji 4246 2822 M ( )S F1S64 Ji 950 2934 M (Denormalizing Output)[77 42 51 51 33 77 41 23 23 43 23 51 45 25 78 49 29 51 49 0]xS 1848 2934 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2552 2934 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3256 2934 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3960 2934 M (........)[22 22 22 22 22 22 22 0]xS 4152 2934 M (10)[47 0]xS F2S64 Ji 4246 2934 M ( )S F1S64 Ji 950 3047 M (Extracting Simple Region SNP Files)[66 46 29 33 41 42 29 23 51 45 25 48 23 77 51 23 42 24 63 42 44 23 51 51 25 48 77 56 25 56 23 23 42 0]xS 2354 3047 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3058 3047 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3762 3047 M (.................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 3047 M (11)[47 0]xS F2S64 Ji 4246 3047 M ( )S F1S64 Ji 950 3159 M (Joining with SNP Classificat)[33 51 23 51 23 51 45 25 67 23 29 51 25 48 77 56 25 64 23 41 36 36 23 32 23 42 41 0]xS 2043 3159 M (ion)[23 51 0]xS 2178 3159 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2882 3159 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3586 3159 M (.........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 3159 M (12)[47 0]xS F2S64 Ji 4246 3159 M ( )S F1S64 Ji 1050 3272 M (The Joined CSV File)[61 51 42 25 33 51 23 51 42 50 25 64 48 68 25 56 23 23 0]xS 1870 3272 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2574 3272 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3278 3272 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3982 3272 M (.......)[22 22 22 22 22 22 0]xS 4152 3272 M (12)[47 0]xS F2S64 Ji 4246 3272 M ( )S F1S64 Ji 1050 3384 M (The Flanking FASTA File)[61 51 42 25 56 23 41 51 47 23 51 45 25 56 68 48 61 68 25 56 23 23 0]xS 2068 3384 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2772 3384 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3476 3384 M (..............................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 3384 M (12)[47 0]xS F2S64 Ji 4246 3384 M ( )S F1S64 Ji 1050 3497 M (Single Case)[48 23 51 45 23 42 25 63 41 36 0]xS 1496 3497 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2200 3497 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2904 3497 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3608 3497 M (........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 3497 M (13)[47 0]xS F2S64 Ji 4246 3497 M ( )S F3S64 Ji 1050 3609 M (By Batch)[56 33 25 56 41 25 27 0]xS F1S64 Ji 1364 3609 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2068 3609 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2772 3609 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3476 3609 M (..............................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 3609 M (13)[47 0]xS F2S64 Ji 4246 3609 M ( )S F1S64 Ji 650 3722 M (Appendix)[68 51 51 42 51 50 23 0]xS 1034 3722 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 1738 3722 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2442 3722 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3146 3722 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3850 3722 M (.............)[22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 3722 M (13)[47 0]xS F2S64 Ji 4246 3722 M ( )S F1S64 Ji 850 3834 M (Showing La)[48 51 51 67 23 51 45 25 57 0]xS 1309 3834 M (test Databases)[29 42 36 29 25 77 41 29 41 51 41 36 42 0]xS 1870 3834 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2574 3834 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3278 3834 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3982 3834 M (.......)[22 22 22 22 22 22 0]xS 4152 3834 M (13)[47 0]xS F2S64 Ji 4246 3834 M ( )S F1S64 Ji 850 3947 M (Classifying SNPs by Genomic Coordinates)[64 23 41 36 36 23 32 42 23 51 45 25 48 77 56 36 25 51 42 25 77 42 51 51 77 23 42 25 64 51 51 33 50 23 51 41 29 42 0]xS 2530 3947 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3234 3947 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3938 3947 M (.........)[22 22 22 22 22 22 22 22 0]xS 4152 3947 M (14)[47 0]xS F2S64 Ji 4246 3947 M ( )S F1S64 Ji 950 4059 M (Classifying Sam\222s SNPs)[64 23 41 36 36 23 32 42 23 51 45 25 48 41 77 22 36 25 48 77 56 0]xS 1870 4059 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2574 4059 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3278 4059 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3982 4059 M (.......)[22 22 22 22 22 22 0]xS 4152 4059 M (14)[47 0]xS F2S64 Ji 4246 4059 M ( )S F1S64 Ji 850 4172 M (Process Overview)[56 33 51 42 42 36 36 25 78 47 42 33 47 23 42 0]xS 1562 4172 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2266 4172 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2970 4172 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3674 4172 M (.....................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 4172 M (16)[47 0]xS F2S64 Ji 4246 4172 M ( )S F1S64 Ji 850 4284 M (SNP Classification Hierarchical Data Output Format)[48 77 56 25 64 23 41 36 36 23 32 23 42 41 29 23 51 51 25 76 23 42 33 41 33 42 51 23 42 41 23 25 77 41 28 41 25 78 49 29 51 49 29 25 56 51 33 77 41 0]xS 2904 4284 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3608 4284 M (........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 4284 M (16)[47 0]xS F2S64 Ji 4246 4284 M ( )S F1S64 Ji 950 4397 M (Hierarchical Annotation Levels)[76 23 42 33 41 33 42 51 23 42 41 23 24 68 51 51 51 29 41 29 23 51 51 25 57 42 47 42 23 0]xS 2178 4397 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2882 4397 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3586 4397 M (.........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 4397 M (17)[47 0]xS F2S64 Ji 4246 4397 M ( )S F1S64 Ji 1050 4509 M (Positional)[56 51 36 23 29 23 51 51 41 0]xS 1452 4509 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2156 4509 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2860 4509 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3564 4509 M (..........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 4509 M (17)[47 0]xS F2S64 Ji 4246 4509 M ( )S F1S64 Ji 1050 4622 M (Gene)[77 42 51 0]xS 1276 4622 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 1980 4622 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2684 4622 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3388 4622 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4092 4622 M (..)[22 0]xS 4152 4622 M (17)[47 0]xS F2S64 Ji 4246 4622 M ( )S F1S64 Ji 1050 4734 M (Transcript)[61 33 41 51 36 42 33 23 51 0]xS 1452 4734 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2156 4734 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2860 4734 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3564 4734 M (..........................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 4734 M (18)[47 0]xS F2S64 Ji 4246 4734 M ( )S F1S64 Ji 1050 4847 M (Protein)[56 33 51 29 42 23 0]xS 1342 4847 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2046 4847 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 2750 4847 M (................................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 3454 4847 M (...............................)[22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 0]xS 4152 4847 M (19)[47 0]xS F2S64 Ji 4246 4847 M ( )S F1S64 Ji 650 4959 M ( )S LH (%%[Page: 2]%%) = %%PageTrailer %%Page: 3 3 %%PageBoundingBox: 12 12 599 779 %%EndPageComments %%BeginPageSetup /DeviceRGB dup setcolorspace /colspABC exch def mysetup concat colspRefresh %%EndPageSetup /DeviceGray dup setcolorspace /colspABC exch def 0 0 scol /F0SC8 F0 [200 0 0 -200 0 0 ] mFS F0SC8 Ji 650 764 M (Introduction)[79 110 63 71 104 110 110 94 63 56 105 0]xS 1725 764 M ( )S F1S64 Ji 650 928 M (The purpose of the SNP Classifier is to determine, on a previously annotated sequence, what ) [61 51 42 25 51 49 33 51 51 36 42 25 51 32 25 29 51 42 25 48 77 56 26 64 23 41 36 36 23 32 23 42 33 25 23 36 25 29 51 25 50 42 29 42 33 77 23 51 42 22 25 51 51 25 41 25 51 33 42 47 23 51 49 36 23 42 25 41 51 51 51 29 41 29 42 49 25 36 42 49 49 42 51 42 42 22 25 67 50 41 29 0]xS 650 1041 M (biological )[51 23 51 23 51 45 23 42 41 23 0]xS 1048 1041 M (impact a specific edit will have )[23 77 50 41 42 29 25 41 25 36 51 42 42 23 32 22 42 25 42 50 23 29 25 67 23 23 23 25 50 41 47 42 0]xS 2251 1041 M (on )[51 51 0]xS 2378 1041 M (a)S 2419 1041 M ( particular position.)[25 50 41 33 29 23 41 49 23 41 33 25 51 51 36 23 29 23 51 51 0]xS 3169 1041 M ( More generally, given an )[25 25 83 51 33 42 25 45 42 51 42 33 41 23 23 42 22 25 45 23 46 42 51 25 41 51 0]xS 650 1153 M (indel or substitution in an annotated sequence, we would like to answer the question of: ) [23 51 50 42 23 25 51 33 25 36 49 51 36 29 23 29 49 29 23 51 51 25 23 51 25 41 51 26 41 51 51 51 29 41 29 42 50 25 36 42 49 49 42 51 41 42 22 25 67 42 24 66 51 49 23 50 25 23 23 47 42 25 29 51 25 41 51 36 67 42 33 25 29 51 42 25 49 48 42 36 29 23 51 51 25 51 32 22 25 0]xS 650 1266 M (Will there be any impact on any resultant protein? This ability to pe) [89 23 23 23 25 29 51 42 33 42 25 51 42 24 41 51 42 25 23 77 51 40 42 29 25 51 51 25 41 51 42 25 33 42 36 49 23 29 41 51 29 25 51 33 51 29 42 23 51 36 25 25 62 51 23 36 25 41 51 23 23 23 29 42 25 29 51 25 51 0]xS 3280 1266 M (rform impact analysis)[33 32 51 33 77 25 23 77 52 41 42 29 25 41 51 41 22 42 36 23 0]xS 4112 1266 M ( )S 650 1378 M (has )[51 41 36 0]xS 803 1378 M (been )[51 42 42 51 0]xS 1014 1378 M (shown to be useful in several applications. Most notably, SNP impact analysis is ) [36 51 51 67 51 25 29 51 25 51 42 25 49 36 42 32 49 23 25 23 51 25 36 42 47 42 33 41 23 25 41 51 51 23 23 41 41 29 23 51 51 36 22 25 25 83 51 36 29 25 51 51 29 41 51 23 42 22 25 48 77 56 25 23 77 51 41 42 29 25 41 51 41 23 42 36 23 36 25 23 36 0]xS 650 1491 M (important in quickly determining the significance of a newly discovered polymorphism after ) [23 77 51 51 33 29 41 51 29 25 23 51 25 49 49 23 42 47 23 42 25 50 42 29 42 32 77 23 51 23 51 45 25 29 51 42 25 36 23 45 51 23 32 23 42 41 51 41 42 25 51 32 25 41 25 51 42 67 23 42 25 49 23 36 42 51 47 42 33 42 50 25 51 51 23 41 77 51 33 51 51 23 36 77 25 41 32 29 42 33 0]xS 650 1603 M (SNP calling or analyzing the)[48 77 56 25 42 41 23 23 23 51 45 25 51 33 25 41 51 41 22 42 43 23 51 45 25 28 51 0]xS 1743 1603 M ( likelihood that a SNP is )[25 23 23 47 42 23 23 51 51 51 50 25 29 51 41 29 25 41 24 48 77 56 25 23 36 0]xS 2707 1603 M (not simply)[51 51 29 25 36 23 77 51 23 0]xS 3115 1603 M ( )S 3140 1603 M (a )[41 0]xS 3206 1603 M (sequencing)[36 42 49 49 42 51 42 23 51 0]xS 3636 1603 M ( or )[25 51 33 0]xS 3770 1603 M (assembly)[41 36 36 42 77 51 23 0]xS 4118 1603 M ( )S 650 1716 M (error)[42 33 33 51 0]xS 842 1716 M (.)S 864 1716 M ( )S 650 1828 M ( )S 650 1941 M (In actually, when we say SNP in this manual, we really mean polymorphism, since the scripts ) [35 51 25 41 42 29 49 41 23 23 42 22 24 67 51 42 51 25 66 42 25 36 41 42 25 47 77 56 25 23 51 25 29 51 23 36 25 77 41 51 49 41 23 22 25 67 42 25 33 42 41 22 23 42 25 77 42 41 51 25 51 51 23 42 77 51 33 51 51 23 36 77 22 25 36 23 51 42 42 25 29 51 42 25 36 42 33 23 51 29 36 0]xS 650 2053 M (deal with multi)[50 42 41 23 25 67 23 29 51 25 77 49 23 29 0]xS 1227 2053 M (-)S 1258 2053 M (nucleotide polymorphism the)[51 49 42 22 42 51 29 23 50 41 25 51 51 23 42 77 51 33 51 51 23 36 77 25 29 51 0]xS 2396 2053 M ( same way. It)[25 36 41 77 42 25 67 41 42 22 25 25 35 0]xS 2928 2053 M ( i)[25 0]xS 2976 2053 M (s just eas)[36 25 23 49 36 29 25 42 41 0]xS 3318 2053 M (ier to say SNP, much )[23 42 33 25 29 51 25 36 41 42 25 48 77 56 22 25 77 49 42 51 0]xS 650 2166 M (like many people in certain geographical regions call all sodas, coke.) [23 23 47 42 25 77 41 51 42 25 50 42 51 51 23 42 25 23 51 25 41 42 33 29 41 22 51 25 45 42 51 45 33 41 51 51 23 41 41 23 25 33 42 45 23 51 51 36 25 42 41 23 22 25 41 23 23 25 36 51 50 41 36 22 25 42 51 47 42 0]xS 3261 2166 M ( )S 650 2278 M ( )S 650 2391 M (There are )[61 51 42 33 42 25 41 33 42 0]xS 1045 2391 M (several programs involved in )[36 42 47 42 33 41 23 25 51 33 51 45 33 41 77 36 25 23 51 47 51 23 47 42 50 25 23 51 0]xS 2184 2391 M (SNP analysis)[48 77 56 25 41 51 41 23 42 36 23 0]xS 2683 2391 M (. These will be covered in this manual)[22 25 25 61 51 42 36 42 25 67 23 23 23 25 51 42 25 42 51 46 42 33 42 50 25 23 50 25 29 51 23 36 25 77 41 51 49 41 0]xS 4166 2391 M ( )S 650 2503 M (as well, although t)[41 36 25 67 42 23 23 22 25 41 23 29 51 51 49 45 51 25 0]xS 1348 2503 M (hey are independent programs)[50 42 42 25 41 33 42 25 22 51 50 42 51 42 51 50 42 51 29 25 51 33 51 45 33 41 77 0]xS 2521 2503 M ( and relatively simple.)[25 41 51 50 25 33 42 23 41 29 23 47 42 23 42 25 36 23 77 51 23 42 0]xS 3357 2503 M ( )[25 0]xS 3407 2503 M ( )S 650 2616 M ( )S F3S64 Ji 650 2728 M (This suite of SNP analysis tools is undeniably linked to the Primer Design paradigm of data management. ) [58 42 23 29 25 29 43 23 25 29 25 35 22 25 50 78 53 25 41 43 41 22 33 29 23 29 25 25 35 36 22 29 25 23 29 25 43 43 41 29 43 23 40 41 22 33 25 22 23 43 52 29 41 25 25 35 25 25 42 29 24 53 30 23 63 29 30 25 73 29 29 23 32 43 25 41 41 30 41 41 23 32 63 25 35 22 25 40 40 25 41 25 63 40 43 41 32 29 63 29 43 25 22 25 0]xS 650 2841 M (Even though the code base is independent and requires a separate thinking process ) [69 34 29 43 25 25 42 35 43 32 42 25 25 42 29 25 27 35 41 29 25 41 41 29 29 25 23 29 25 22 43 41 29 41 29 43 41 29 43 25 24 41 43 41 25 30 29 42 43 23 30 29 29 25 41 25 29 29 41 40 30 41 25 29 25 25 42 23 43 52 23 43 32 25 41 30 35 27 29 29 29 0]xS 3362 2841 M (from it )[22 30 35 63 25 23 25 0]xS 3610 2841 M (\(in terms of )[27 23 43 25 25 29 30 63 29 25 35 22 0]xS 4011 2841 M (the )[25 42 29 0]xS 650 2953 M (required )[30 29 43 43 23 30 29 41 0]xS 943 2953 M (understanding of biology\))[43 43 41 29 30 29 25 41 42 41 23 43 32 25 35 22 25 41 23 35 22 35 32 33 0]xS 1760 2953 M ( and )[25 41 43 41 0]xS 1935 2953 M (can)[27 41 0]xS 2046 2953 M ( be used without ever doing primer design, the flow of data from ) [25 41 29 25 43 29 29 41 25 53 23 24 42 35 43 25 25 29 34 29 30 25 41 35 23 43 32 25 41 30 23 63 29 30 25 41 29 29 23 32 43 22 25 25 42 29 25 22 22 35 53 25 35 22 25 41 41 25 41 25 22 30 35 63 0]xS 650 3066 M (Primer Design into SNP Classification cannot be )[53 30 23 63 29 30 25 73 29 29 23 32 43 25 23 43 25 35 25 50 78 53 25 63 22 41 29 29 23 22 23 27 41 25 23 35 43 25 27 41 43 43 35 25 25 41 29 0]xS 2319 3066 M (completely )[27 35 63 40 22 29 25 29 22 33 0]xS 2669 3066 M (ignored and)[23 32 43 35 30 29 41 25 41 43 0]xS 3052 3066 M ( will be noted when appropriate, in )[25 53 23 22 22 25 41 29 25 43 35 25 29 41 25 53 42 29 43 24 41 41 41 30 35 41 30 23 41 25 29 22 25 23 43 0]xS 650 3178 M (italics)[23 25 41 22 23 27 0]xS 840 3178 M (.)S 862 3178 M ( )S F0SC8 Ji 650 3477 M (SNP Classification)[102 169 123 50 135 52 96 83 83 56 61 56 94 96 63 56 104 0]xS 2239 3477 M ( )S F1S64 Ji 650 3641 M (SNP Classification is broken down into two separate progr)[48 77 56 25 64 23 41 36 36 23 32 23 42 41 29 23 51 51 25 23 36 25 51 33 51 47 42 51 25 50 51 67 51 25 23 51 29 51 25 29 67 51 25 36 42 51 41 33 41 28 42 25 51 33 51 45 0]xS 2927 3641 M (ams. The first program is )[41 77 36 22 25 25 61 51 42 25 32 23 33 37 29 25 51 33 52 45 33 41 77 25 23 36 0]xS 650 3753 M (responsible for accumulating annotation from Ensembl and the second program is ) [33 42 36 51 51 51 36 23 51 23 42 25 32 51 33 25 41 42 42 49 77 49 23 41 29 23 51 45 25 41 51 51 51 29 41 29 23 51 51 25 32 33 51 77 25 66 51 36 42 77 51 23 25 41 51 50 25 29 51 42 25 36 42 42 51 51 50 25 51 33 51 45 33 41 77 25 23 36 0]xS 650 3866 M (responsible for generating the SNP classifications based on the downloaded annotation ) [33 42 36 51 51 51 36 23 51 23 42 25 32 51 33 25 45 42 51 42 33 41 29 23 51 45 25 29 51 42 25 48 77 56 25 42 23 41 36 36 23 32 23 42 41 29 23 51 51 36 25 51 41 36 42 50 25 51 51 25 29 51 42 25 50 51 67 51 23 51 41 50 42 50 24 40 51 51 51 29 41 29 23 51 51 0]xS 650 3978 M (information.)[23 51 32 51 33 77 41 29 23 51 51 0]xS 1134 3978 M ( )S F0S96 Ji 650 4234 M (Algorithm Overview )[98 39 81 78 52 42 47 83 127 38 119 69 70 51 69 42 70 106 0]xS 1969 4234 M ( )S F1S64 Ji 650 4384 M (The algorithm for SNP classific)[61 51 42 25 41 23 45 51 33 23 29 51 77 25 32 51 33 25 48 77 56 25 42 24 41 36 36 23 32 23 0]xS 1873 4384 M (ation is fairly straightforward. It is essentially )[41 29 23 51 51 25 23 36 25 32 41 23 33 23 42 25 36 29 33 41 23 45 51 29 32 51 33 67 41 33 50 22 25 25 35 29 25 23 36 25 42 37 36 42 51 29 23 41 23 23 42 0]xS 3649 4384 M (a decision tree )[41 25 50 42 42 23 36 23 51 51 25 29 33 42 42 0]xS 650 4497 M (that drills down through the functional class of a sequence. Since the relationship between ) [29 51 41 29 25 50 33 23 23 23 36 25 50 51 67 51 25 29 51 33 51 49 45 51 25 30 51 42 25 32 49 51 42 29 23 51 51 41 23 25 42 22 41 36 36 25 51 32 25 41 25 36 42 49 49 42 51 42 42 22 25 25 48 23 50 42 42 25 29 51 42 25 33 42 22 41 29 23 51 50 36 51 23 51 25 51 42 29 67 42 42 51 0]xS 650 4609 M (gene and transcript is one)[45 42 51 42 25 41 51 50 25 29 33 41 51 36 42 33 23 51 29 25 23 36 25 51 51 0]xS 1643 4609 M (-)S 1674 4609 M (to)[29 0]xS 1754 4609 M (-)S 1785 4609 M (many, the decision tree branch points contain loops to cycle ) [77 41 51 42 22 25 29 51 42 25 50 42 42 23 36 23 51 51 25 29 33 42 42 25 51 33 41 51 42 51 25 51 51 23 51 29 36 25 42 51 51 29 41 23 51 25 23 50 51 51 36 25 29 51 25 42 42 42 23 42 0]xS 650 4722 M (thro)[29 51 33 0]xS 814 4722 M (ugh each relationship. )[49 45 51 25 42 41 42 51 25 33 42 23 41 29 23 51 51 36 51 23 51 21 25 0]xS 1710 4722 M ( )S 650 4834 M ( )S 650 4947 M (The goal of the algorithm was to produce as much useful information as possible to remove ) [61 51 42 25 45 51 41 23 25 51 32 25 29 51 42 25 41 23 45 51 33 23 29 51 77 25 67 41 36 25 29 51 25 51 33 51 50 49 42 42 25 41 36 25 77 49 42 51 25 49 36 42 32 49 23 25 23 51 32 51 33 77 41 29 23 51 51 25 41 36 25 51 51 37 36 24 51 23 42 25 29 51 25 33 42 77 51 47 42 0]xS 650 5059 M (manual curation. It could take )[77 41 51 49 41 23 25 42 49 33 41 29 23 51 51 22 25 25 35 29 25 42 51 49 23 49 25 29 41 47 42 0]xS 1860 5059 M (hours)[51 51 49 33 0]xS 2080 5059 M ( )S 2105 5059 M (for a person )[32 51 33 25 41 25 51 42 33 36 51 51 0]xS 2601 5059 M (to perform the same calculations )[30 51 25 51 42 33 32 51 33 77 25 29 51 42 25 36 41 77 42 25 42 41 23 42 49 22 41 29 23 51 51 36 0]xS 3894 5059 M (simply)[36 23 77 51 23 0]xS 4146 5059 M ( )S 650 5172 M (because of the confusion wrought from coordinate )[51 42 42 41 49 36 42 25 51 32 25 29 51 42 25 42 51 51 32 49 36 23 51 51 25 67 33 51 49 45 51 29 25 32 33 51 77 25 42 51 51 33 50 23 51 41 29 42 0]xS 2650 5172 M (translations, reverse complementation, )[29 33 41 51 36 23 41 29 23 51 51 36 22 25 33 42 47 42 33 36 42 25 42 51 77 51 23 42 77 42 51 29 41 29 23 51 51 22 0]xS 650 5284 M (and lookup tables.)[41 51 50 25 23 51 51 47 49 51 25 29 41 51 23 42 36 0]xS 1358 5284 M ( )[25 0]xS 1408 5284 M ( )S 650 5397 M ( )S 650 5509 M (The following diagram illustrates the possible paths a polymorphism can take on its road ) [61 51 42 25 32 51 23 23 51 67 23 51 45 25 50 23 41 45 33 41 77 25 23 23 23 48 36 29 33 41 29 42 36 25 29 51 42 25 51 51 37 36 23 51 23 42 25 51 41 29 51 36 26 41 25 51 51 23 42 77 51 33 51 51 23 36 77 25 42 41 51 25 29 41 47 42 24 51 51 25 23 29 36 25 33 51 41 50 0]xS 650 5622 M (towards enlightenment. )[29 51 67 41 33 50 36 25 42 51 23 23 45 51 29 42 51 77 42 51 29 22 25 0]xS 1610 5622 M ( )S 650 5734 M ( )S 2450 5847 M ( )S LH (%%[Page: 3]%%) = %%PageTrailer %%Page: 4 4 %%PageBoundingBox: 12 12 599 779 %%EndPageComments %%BeginPageSetup /DeviceRGB dup setcolorspace /colspABC exch def mysetup concat colspRefresh %%EndPageSetup Pscript_WinNT_Incr begin %%BeginResource: file Pscript_Win_GdiObject 5.0 0 /SavedCTM null d/CTMsave{/SavedCTM SavedCTM currentmatrix d}b/CTMrestore {SavedCTM setmatrix}b/mp null d/ADO_mxRot null d/GDIHMatrix null d /GDIHPatternDict 22 dict d GDIHPatternDict `/PatternType 1 d/PaintType 2 d/Reps L2?{1}{5}? d/XStep 8 Reps mul d/YStep XStep d/BBox[0 0 XStep YStep]d/TilingType 1 d/PaintProc{` 1 Lw[]0 sd PaintData , exec E}b/FGnd null d/BGnd null d /HS_Horizontal{horiz}b/HS_Vertical{vert}b/HS_FDiagonal{fdiag}b/HS_BDiagonal {biag}b/HS_Cross{horiz vert}b/HS_DiagCross{fdiag biag}b/MaxXYStep XStep YStep gt{XStep}{YStep}? d/horiz{Reps{0 4 M XStep 0 - 0 8 +}repeat 0 -8 Reps mul + K}b /vert{Reps{4 0 M 0 YStep - 8 0 +}repeat 0 -8 Reps mul + K}b/biag{Reps{0 0 M MaxXYStep @ - 0 YStep neg M MaxXYStep @ - 0 8 +}repeat 0 -8 Reps mul + 0 YStep M 8 8 - K}b/fdiag{Reps{0 0 M MaxXYStep @ neg - 0 YStep M MaxXYStep @ neg - 0 8 +}repeat 0 -8 Reps mul + MaxXYStep @ M 8 -8 - K}b E/makehatch{4 -2 $/yOrg ~ d /xOrg ~ d GDIHPatternDict/PaintData 3 -1 $ put CTMsave GDIHMatrix setmatrix GDIHPatternDict matrix xOrg yOrg + mp CTMrestore ~ U ~ 2 ^ put}b/h0{/h0 /HS_Horizontal makehatch}b/h1{/h1/HS_Vertical makehatch}b/h2{/h2/HS_FDiagonal makehatch}b/h3{/h3/HS_BDiagonal makehatch}b/h4{/h4/HS_Cross makehatch}b/h5{/h5 /HS_DiagCross makehatch}b/GDIBWPatternMx null d/pfprep{save 8 1 $ /PatternOfTheDay 8 1 $ GDIBWPatternDict `/yOrg ~ d/xOrg ~ d/PaintData ~ d/yExt ~ d/Width ~ d/BGnd ~ d/FGnd ~ d/Height yExt RepsV mul d/mx[Width 0 0 Height 0 0]d E build_pattern ~ !}b/pfbf{/fEOFill ~ d pfprep hbf fEOFill{O}{L}? restore}b /GraphInit{GDIHMatrix null eq{/SavedCTM matrix d : ADO_mxRot concat 0 0 snap + : 0.48 @ GDIHPatternDict ` YStep mul ~ XStep mul ~ nonzero_dsnap YStep V ~ XStep V ~ E +S/GDIHMatrix matrix currentmatrix readonly d ; : 0.24 -0.24 +S GDIBWPatternDict ` Width Height E nonzero_dsnap +S/GDIBWPatternMx matrix currentmatrix readonly d ; ;}if}b %%EndResource %%BeginResource: file Pscript_Win_GdiObject_L3 5.0 0 /GDIBWPatternDict 25 dict @ `/PatternType 1 d/PaintType 1 d/RepsV 1 d/RepsH 1 d /BBox[0 0 RepsH 1]d/TilingType 1 d/XStep 1 d/YStep 1 d/Height 8 RepsV mul d /Width 8 d/mx[Width 0 0 Height neg 0 Height]d/FGnd null d/BGnd null d /SetBGndFGnd{BGnd null ne{BGnd aload ! scol BBox aload ! 2 ^ sub ~ 3 ^ sub ~ rf}if FGnd null ne{FGnd aload ! scol}if}b/PaintProc{` SetBGndFGnd RepsH{Width Height F mx PaintData imagemask Width 0 +}repeat E}b E d/mp/makepattern , d /build_pattern{CTMsave GDIBWPatternMx setmatrix/nupangle where{! nupangle -90 eq{nupangle R}if}if GDIBWPatternDict @ ` Width Height ne{Width Height gt{Width Height V 1}{1 Height Width V}? +S}if xOrg yOrg E matrix + mp CTMrestore}b/hbf {setpattern}b/hf{:/fEOFill ~ d ~ ! setpattern fEOFill{O}{L}? ;}b/pbf{: ! /fEOFill ~ d GDIBWPatternDict `/yOrg ~ d/xOrg ~ d/PaintData ~ d/OutputBPP ~ d /Height ~ d/Width ~ d/PaintType 1 d/PatternType 1 d/TilingType 1 d/BBox[0 0 Width Height]d/XStep Width d/YStep Height d/mx xOrg yOrg matrix + d 20 dict @ ` /ImageType 1 d/Width Width d/Height Height d/ImageMatrix[1 0 0 1 0 0]d /BitsPerComponent 8 d OutputBPP 24 eq{/Decode[0 1 0 1 0 1]d}{OutputBPP 8 eq{ /Decode[0 1]d}{/Decode[0 1 0 1 0 1 0 1]d}?}?/DataSource{PaintData}d E/ImageDict ~ d/PaintProc{` ImageDict image E}b & mx makepattern setpattern E fEOFill{O}{L} ? ;}b/mask_pbf{:/fEOFill ~ d 20 dict `/yOrg ~ d/xOrg ~ d/PaintData ~ d/Height ~ d/Width ~ d/PatternType 1 d/PaintType 2 d/TilingType 1 d/BBox[0 0 Width Height] d/XStep Width d/YStep Height d/mx xOrg yOrg matrix + d/PaintProc{` Width Height T 1 1 dtransform abs ~ abs ~ 0 0 3 -1 $ 0 0 6 array astore{PaintData}imagemask E}b & mx makepattern setpattern E fEOFill{O}{L}? ;}b/grf4{4 dict `/ShadingType 4 d/DataSource ~ d/ColorSpace ~ d & E shfill}b %%EndResource end reinitialize /DeviceGray dup setcolorspace /colspABC exch def : N 1814 520 485 242 rp C 1 0 scol L ; 0 0 scol 1 Lj 1 Lc 21 Lw solid N 1814 762 M 1814 520 I 2299 520 I 2299 762 I 1814 762 I C : 0.996 1 +S K ; %%IncludeResource: font Arial-Bold 7500 VM? /Arial-Bold FontHasEuro not { /Euro.Arial-Bold [556 0 12 -19 563 710 ] <97F8C00DDBF7240378F70401F774EA01F803EA01F8EAF70401F8BBF9011571B141BE278B 08FB278B303173FB32085906642C05DB0676078B828C828B82086206632C05E506A8FB3A EC3EF71B8B08C18BC192B9A908F71407676C54754C8B083B8B6ED483C508F72C06B3EA05 FB5E06BB07F77106B3EA05FB91069AE5B2B9CC8B08C98BB26FA17408A07691828F830809 0E> AddEuroGlyph /Euro /Arial-Bold /Arial-Bold-Copy BuildNewFont } if F /F4 0 /256 T /Arial-Bold mF /F4S37 F4 [55.086 0 0 -55.086 0 0 ] mFS F4S37 Ji 1870 627 M (Polymorphism)[35 35 16 30 50 35 21 35 35 15 30 0]xS 1951 687 M (Position)[35 35 30 15 20 16 35 0]xS : N 1451 1006 484 243 rp C 1 0 scol L ; 5 Lw N 1451 1249 M 1451 1006 I 1935 1006 I 1935 1249 I 1451 1249 I C : 0.996 1 +S K ; %%IncludeResource: font Arial 7500 VM? /Arial FontHasEuro not { /Euro.Arial [556 0 24 -19 541 703 ] AddEuroGlyph /Euro /Arial /Arial-Copy BuildNewFont } if F /F5 0 /256 T /Arial mF /F5S37 F5 [55.086 0 0 -55.086 0 0 ] mFS F5S37 Ji 1573 1142 M (Intergenic)[15 30 15 30 21 30 30 30 10 0]xS N 2057 762 M 2057 915 I 1693 915 I 1693 1006 I : 0.996 1 +S K ; : N 1058 915 302 243 rp C 1 0 scol L ; N 1058 1158 M 1058 915 I 1360 915 I 1360 1158 I 1058 1158 I C : 0.996 1 +S K ; 1090 1021 M (Repetitive)[40 31 30 30 15 10 15 11 24 0]xS 1125 1086 M (Region)[41 30 30 10 30 0]xS N 1814 644 M 1779 644 I 1778 644 I 1777 643 I 1777 642 I 1776 641 I 1777 640 I 1777 639 I 1778 639 I 1779 639 I 1814 639 I 1815 639 I 1816 639 I 1817 640 I 1817 641 I 1817 642 I 1816 643 I 1815 644 I 1814 644 I 1814 644 I C 1754 644 M 1719 644 I 1718 644 I 1717 643 I 1716 642 I 1716 641 I 1716 640 I 1717 639 I 1718 639 I 1719 639 I 1754 639 I 1755 639 I 1756 639 I 1756 640 I 1756 641 I 1756 642 I 1756 643 I 1755 644 I 1754 644 I 1754 644 I C 1693 644 M 1658 644 I 1657 644 I 1656 643 I 1656 642 I 1656 641 I 1656 640 I 1656 639 I 1657 639 I 1658 639 I 1693 639 I 1694 639 I 1695 639 I 1696 640 I 1696 641 I 1696 642 I 1695 643 I 1694 644 I 1693 644 I 1693 644 I C 1633 644 M 1598 644 I 1597 644 I 1596 643 I 1595 642 I 1595 641 I 1595 640 I 1596 639 I 1597 639 I 1598 639 I 1633 639 I 1634 639 I 1635 639 I 1635 640 I 1635 641 I 1635 642 I 1635 643 I 1634 644 I 1633 644 I 1633 644 I C 1572 644 M 1537 644 I 1536 644 I 1535 643 I 1535 642 I 1535 641 I 1535 640 I 1535 639 I 1536 639 I 1537 639 I 1572 639 I 1574 639 I 1574 639 I 1575 640 I 1575 641 I 1575 642 I 1574 643 I 1574 644 I 1572 644 I 1572 644 I C 1512 644 M 1477 644 I 1476 644 I 1475 643 I 1474 642 I 1474 641 I 1474 640 I 1475 639 I 1476 639 I 1477 639 I 1512 639 I 1513 639 I 1514 639 I 1514 640 I 1515 641 I 1514 642 I 1514 643 I 1513 644 I 1512 644 I 1512 644 I C 1452 644 M 1416 644 I 1415 644 I 1415 643 I 1414 642 I 1414 641 I 1414 640 I 1415 639 I 1415 639 I 1416 639 I 1452 639 I 1453 639 I 1453 639 I 1454 640 I 1454 641 I 1454 642 I 1453 643 I 1453 644 I 1452 644 I 1452 644 I C 1391 644 M 1356 644 I 1355 644 I 1354 643 I 1354 642 I 1353 641 I 1354 640 I 1354 639 I 1355 639 I 1356 639 I 1391 639 I 1392 639 I 1393 639 I 1393 640 I 1394 641 I 1393 642 I 1393 643 I 1392 644 I 1391 644 I 1391 644 I C 1331 644 M 1295 644 I 1295 644 I 1294 643 I 1293 642 I 1293 641 I 1293 640 I 1294 639 I 1295 639 I 1295 639 I 1331 639 I 1332 639 I 1333 639 I 1333 640 I 1333 641 I 1333 642 I 1333 643 I 1332 644 I 1331 644 I 1331 644 I C 1271 644 M 1236 644 I 1235 644 I 1234 643 I 1234 642 I 1233 641 I 1234 640 I 1234 639 I 1235 639 I 1236 639 I 1271 639 I 1272 639 I 1273 639 I 1274 640 I 1274 641 I 1274 642 I 1273 643 I 1272 644 I 1271 644 I 1271 644 I C 1211 644 M 1210 644 I 1212 641 I 1212 675 I 1212 676 I 1211 677 I 1211 678 I 1210 678 I 1209 678 I 1208 677 I 1207 676 I 1207 675 I 1207 641 I 1207 640 I 1208 639 I 1209 639 I 1210 639 I 1211 639 I 1212 639 I 1213 639 I 1213 640 I 1213 641 I 1213 642 I 1213 643 I 1212 644 I 1211 644 I 1211 644 I C 1212 700 M 1212 736 I 1212 737 I 1211 737 I 1211 738 I 1210 738 I 1209 738 I 1208 737 I 1207 737 I 1207 736 I 1207 700 I 1207 699 I 1208 699 I 1209 698 I 1210 698 I 1211 698 I 1211 699 I 1212 699 I 1212 700 I 1212 700 I C 1212 761 M 1212 797 I 1212 798 I 1211 799 I 1211 799 I 1210 800 I 1209 799 I 1208 799 I 1207 798 I 1207 797 I 1207 761 I 1207 760 I 1208 759 I 1209 758 I 1210 758 I 1211 758 I 1211 759 I 1212 760 I 1212 761 I 1212 761 I C 1212 822 M 1212 858 I 1212 858 I 1211 859 I 1211 860 I 1210 860 I 1209 860 I 1208 859 I 1207 858 I 1207 858 I 1207 822 I 1207 821 I 1208 820 I 1209 820 I 1210 820 I 1211 820 I 1211 820 I 1212 821 I 1212 822 I 1212 822 I C 1212 883 M 1212 915 I 1212 916 I 1211 917 I 1211 917 I 1210 918 I 1209 917 I 1208 917 I 1207 916 I 1207 915 I 1207 883 I 1207 882 I 1208 881 I 1209 880 I 1210 880 I 1211 880 I 1211 881 I 1212 882 I 1212 883 I 1212 883 I C : L ; : 0.996 1 +S K ; : N 665 915 302 243 rp C 1 0 scol L ; N 665 1158 M 665 915 I 967 915 I 967 1158 I 665 1158 I C : 0.996 1 +S K ; 733 1051 M (dbSNP)[30 30 35 41 0]xS N 1814 644 M 1779 644 I 1778 644 I 1777 643 I 1777 642 I 1776 641 I 1777 640 I 1777 639 I 1778 639 I 1779 639 I 1814 639 I 1815 639 I 1816 639 I 1817 640 I 1817 641 I 1817 642 I 1816 643 I 1815 644 I 1814 644 I 1814 644 I C 1754 644 M 1719 644 I 1718 644 I 1717 643 I 1716 642 I 1716 641 I 1716 640 I 1717 639 I 1718 639 I 1719 639 I 1754 639 I 1755 639 I 1756 639 I 1756 640 I 1756 641 I 1756 642 I 1756 643 I 1755 644 I 1754 644 I 1754 644 I C 1693 644 M 1658 644 I 1657 644 I 1656 643 I 1656 642 I 1656 641 I 1656 640 I 1656 639 I 1657 639 I 1658 639 I 1693 639 I 1694 639 I 1695 639 I 1696 640 I 1696 641 I 1696 642 I 1695 643 I 1694 644 I 1693 644 I 1693 644 I C 1633 644 M 1598 644 I 1597 644 I 1596 643 I 1595 642 I 1595 641 I 1595 640 I 1596 639 I 1597 639 I 1598 639 I 1633 639 I 1634 639 I 1635 639 I 1635 640 I 1635 641 I 1635 642 I 1635 643 I 1634 644 I 1633 644 I 1633 644 I C 1572 644 M 1537 644 I 1536 644 I 1535 643 I 1535 642 I 1535 641 I 1535 640 I 1535 639 I 1536 639 I 1537 639 I 1572 639 I 1574 639 I 1574 639 I 1575 640 I 1575 641 I 1575 642 I 1574 643 I 1574 644 I 1572 644 I 1572 644 I C 1512 644 M 1477 644 I 1476 644 I 1475 643 I 1474 642 I 1474 641 I 1474 640 I 1475 639 I 1476 639 I 1477 639 I 1512 639 I 1513 639 I 1514 639 I 1514 640 I 1515 641 I 1514 642 I 1514 643 I 1513 644 I 1512 644 I 1512 644 I C 1452 644 M 1416 644 I 1415 644 I 1415 643 I 1414 642 I 1414 641 I 1414 640 I 1415 639 I 1415 639 I 1416 639 I 1452 639 I 1453 639 I 1453 639 I 1454 640 I 1454 641 I 1454 642 I 1453 643 I 1453 644 I 1452 644 I 1452 644 I C 1391 644 M 1356 644 I 1355 644 I 1354 643 I 1354 642 I 1353 641 I 1354 640 I 1354 639 I 1355 639 I 1356 639 I 1391 639 I 1392 639 I 1393 639 I 1393 640 I 1394 641 I 1393 642 I 1393 643 I 1392 644 I 1391 644 I 1391 644 I C 1331 644 M 1295 644 I 1295 644 I 1294 643 I 1293 642 I 1293 641 I 1293 640 I 1294 639 I 1295 639 I 1295 639 I 1331 639 I 1332 639 I 1333 639 I 1333 640 I 1333 641 I 1333 642 I 1333 643 I 1332 644 I 1331 644 I 1331 644 I C 1271 644 M 1236 644 I 1235 644 I 1234 643 I 1234 642 I 1233 641 I 1234 640 I 1234 639 I 1235 639 I 1236 639 I 1271 639 I 1272 639 I 1273 639 I 1274 640 I 1274 641 I 1274 642 I 1273 643 I 1272 644 I 1271 644 I 1271 644 I C 1211 644 M 1176 644 I 1175 644 I 1174 643 I 1173 642 I 1173 641 I 1173 640 I 1174 639 I 1175 639 I 1176 639 I 1211 639 I 1212 639 I 1213 639 I 1213 640 I 1213 641 I 1213 642 I 1213 643 I 1212 644 I 1211 644 I 1211 644 I C 1150 644 M 1115 644 I 1114 644 I 1113 643 I 1113 642 I 1113 641 I 1113 640 I 1113 639 I 1114 639 I 1115 639 I 1150 639 I 1151 639 I 1152 639 I 1153 640 I 1153 641 I 1153 642 I 1152 643 I 1151 644 I 1150 644 I 1150 644 I C 1090 644 M 1055 644 I 1054 644 I 1053 643 I 1052 642 I 1052 641 I 1052 640 I 1053 639 I 1054 639 I 1055 639 I 1090 639 I 1091 639 I 1092 639 I 1092 640 I 1092 641 I 1092 642 I 1092 643 I 1091 644 I 1090 644 I 1090 644 I C 1029 644 M 994 644 I 993 644 I 993 643 I 992 642 I 992 641 I 992 640 I 993 639 I 993 639 I 994 639 I 1029 639 I 1031 639 I 1031 639 I 1032 640 I 1032 641 I 1032 642 I 1031 643 I 1031 644 I 1029 644 I 1029 644 I C 969 644 M 934 644 I 933 644 I 932 643 I 931 642 I 931 641 I 931 640 I 932 639 I 933 639 I 934 639 I 969 639 I 970 639 I 971 639 I 971 640 I 972 641 I 971 642 I 971 643 I 970 644 I 969 644 I 969 644 I C 909 644 M 873 644 I 872 644 I 872 643 I 871 642 I 871 641 I 871 640 I 872 639 I 872 639 I 873 639 I 909 639 I 910 639 I 910 639 I 911 640 I 911 641 I 911 642 I 910 643 I 910 644 I 909 644 I 909 644 I C 848 644 M 816 644 I 819 641 I 819 644 I 818 645 I 818 646 I 817 646 I 816 647 I 815 646 I 814 646 I 814 645 I 814 644 I 814 641 I 814 640 I 814 639 I 815 639 I 816 639 I 848 639 I 849 639 I 850 639 I 851 640 I 851 641 I 851 642 I 850 643 I 849 644 I 848 644 I 848 644 I C 819 669 M 819 704 I 818 706 I 818 706 I 817 707 I 816 707 I 815 707 I 814 706 I 814 706 I 814 704 I 814 669 I 814 668 I 814 668 I 815 667 I 816 667 I 817 667 I 818 668 I 818 668 I 819 669 I 819 669 I C 819 730 M 819 765 I 818 766 I 818 767 I 817 767 I 816 767 I 815 767 I 814 767 I 814 766 I 814 765 I 814 730 I 814 729 I 814 728 I 815 727 I 816 727 I 817 727 I 818 728 I 818 729 I 819 730 I 819 730 I C 819 791 M 819 826 I 818 827 I 818 828 I 817 829 I 816 829 I 815 829 I 814 828 I 814 827 I 814 826 I 814 791 I 814 789 I 814 788 I 815 788 I 816 788 I 817 788 I 818 788 I 818 789 I 819 791 I 819 791 I C 819 852 M 819 887 I 818 888 I 818 889 I 817 889 I 816 889 I 815 889 I 814 889 I 814 888 I 814 887 I 814 852 I 814 851 I 814 850 I 815 849 I 816 849 I 817 849 I 818 850 I 818 851 I 819 852 I 819 852 I C 819 912 M 819 915 I 818 916 I 818 917 I 817 917 I 816 918 I 815 917 I 814 917 I 814 916 I 814 915 I 814 912 I 814 911 I 814 910 I 815 910 I 816 909 I 817 910 I 818 910 I 818 911 I 819 912 I 819 912 I C : L ; : 0.996 1 +S K ; : N 2117 1006 484 243 rp C 1 0 scol L ; N 2117 1249 M 2117 1006 I 2601 1006 I 2601 1249 I 2117 1249 I C : 0.996 1 +S K ; F4S37 Ji 2212 1112 M (Transcripts)[36 20 30 35 31 30 20 15 35 19 0]xS F5S37 Ji 2273 1177 M (\(Gene\))[20 40 31 30 30 0]xS : N 2117 1522 484 243 rp C 1 0 scol L ; N 2117 1765 M 2117 1522 I 2601 1522 I 2601 1765 I 2117 1765 I C : 0.996 1 +S K ; 2177 1662 M (Intronic Region)[15 30 16 20 30 30 10 25 16 40 30 30 10 31 0]xS N 2359 1249 M 2359 1522 I : 0.996 1 +S K ; : N 2843 1522 484 243 rp C 1 0 scol L ; N 2843 1765 M 2843 1522 I 3327 1522 I 3327 1765 I 2843 1765 I C : 0.996 1 +S K ; 2912 1662 M (Exonic Region)[35 25 30 30 10 26 15 40 30 31 10 30 0]xS N 2359 1249 M 2359 1431 I 3085 1431 I 3085 1522 I : 0.996 1 +S K ; : N 1390 1522 485 243 rp C 1 0 scol L ; N 1390 1765 M 1390 1522 I 1875 1522 I 1875 1765 I 1390 1765 I C : 0.996 1 +S K ; 1517 1626 M (Upstream)[41 30 25 15 20 31 30 0]xS 1427 1692 M (Promoter Region)[35 20 30 46 30 15 30 20 15 41 30 30 10 30 0]xS N 2359 1249 M 2359 1431 I 1633 1431 I 1633 1522 I : 0.996 1 +S K ; N 2057 762 M 2057 915 I 2359 915 I 2359 1006 I : 0.996 1 +S K ; : N 3569 1522 484 243 rp C 1 0 scol L ; N 3569 1765 M 3569 1522 I 4053 1522 I 4053 1765 I 3569 1765 I C : 0.996 1 +S K ; 3662 1626 M (Downstream)[39 31 40 30 25 15 20 31 30 0]xS 3602 1692 M (Transcript Region)[35 20 30 29 26 25 20 10 30 15 15 41 30 30 10 30 0]xS N 2359 1249 M 2359 1431 I 3811 1431 I 3811 1522 I : 0.996 1 +S K ; : N 1814 1947 485 244 rp C 1 0 scol L ; N 1814 2191 M 1814 1947 I 2299 1947 I 2299 2191 I 1814 2191 I C : 0.996 1 +S K ; 1900 2054 M (5' Splice Site)[30 10 16 35 30 10 10 25 31 15 35 10 15 0]xS 1971 2116 M (Region)[40 30 30 10 31 0]xS N 2359 1765 M 2359 1856 I 2057 1856 I 2057 1947 I : 0.996 1 +S K ; : N 2420 1947 483 244 rp C 1 0 scol L ; N 2420 2191 M 2420 1947 I 2903 1947 I 2903 2191 I 2420 2191 I C : 0.996 1 +S K ; 2509 2054 M (3' Splice Site)[30 10 15 35 30 11 10 25 30 15 35 10 16 0]xS 2574 2116 M (Region)[40 31 30 10 30 0]xS N 2359 1765 M 2359 1856 I 2661 1856 I 2661 1947 I : 0.996 1 +S K ; : N 2843 2798 484 243 rp C 1 0 scol L ; N 2843 3041 M 2843 2798 I 3327 2798 I 3327 3041 I 2843 3041 I C : 0.996 1 +S K ; 3027 2938 M (CDS)[41 40 0]xS N 3085 1765 M 3085 2798 I : 0.996 1 +S K ; : N 3388 2464 483 242 rp C 1 0 scol L ; N 3388 2706 M 3388 2464 I 3871 2464 I 3871 2706 I 3388 2706 I C : 0.996 1 +S K ; 3546 2600 M (3' UTR)[30 10 16 40 34 0]xS N 3085 1765 M 3085 2373 I 3630 2373 I 3630 2464 I : 0.996 1 +S K ; : N 2299 2464 483 242 rp C 1 0 scol L ; N 2299 2706 M 2299 2464 I 2782 2464 I 2782 2706 I 2299 2706 I C : 0.996 1 +S K ; 2459 2600 M (5' UTR)[30 10 15 40 35 0]xS N 3085 1765 M 3085 2373 I 2540 2373 I 2540 2464 I : 0.996 1 +S K ; : N 2177 3223 484 244 rp C 1 0 scol L ; N 2177 3467 M 2177 3223 I 2661 3223 I 2661 3467 I 2177 3467 I C : 0.996 1 +S K ; 2278 3362 M (Substitution)[35 30 31 25 15 10 15 29 15 10 31 0]xS N 3085 3041 M 3085 3132 I 2420 3132 I 2420 3223 I : 0.996 1 +S K ; : N 3448 3223 484 244 rp C 1 0 scol L ; N 3448 3467 M 3448 3223 I 3932 3223 I 3932 3467 I 3448 3467 I C : 0.996 1 +S K ; 3632 3362 M (Indel)[15 29 30 31 0]xS N 3085 3041 M 3085 3132 I 3690 3132 I 3690 3223 I : 0.996 1 +S K ; : N 1875 3649 484 242 rp C 1 0 scol L ; N 1875 3891 M 1875 3649 I 2359 3649 I 2359 3891 I 1875 3891 I C : 0.996 1 +S K ; 1961 3785 M (Synonymous)[35 25 30 30 31 25 45 30 31 0]xS N 2420 3467 M 2420 3558 I 2117 3558 I 2117 3649 I : 0.996 1 +S K ; : N 2480 3649 484 242 rp C 1 0 scol L ; N 2480 3891 M 2480 3649 I 2964 3649 I 2964 3891 I 2480 3891 I C : 0.996 1 +S K ; 2519 3785 M (Nonsynonymous)[40 30 30 26 25 30 30 30 26 45 30 30 0]xS N 2420 3467 M 2420 3558 I 2722 3558 I 2722 3649 I : 0.996 1 +S K ; : N 2177 4074 484 243 rp C 1 0 scol L ; N 2177 4317 M 2177 4074 I 2661 4074 I 2661 4317 I 2177 4317 I C : 0.996 1 +S K ; 2288 4209 M (Conserved)[40 30 31 25 30 20 24 31 0]xS N 2722 3891 M 2722 3982 I 2420 3982 I 2420 4074 I : 0.996 1 +S K ; : N 2782 4074 485 243 rp C 1 0 scol L ; N 2782 4317 M 2782 4074 I 3267 4074 I 3267 4317 I 2782 4317 I C : 0.996 1 +S K ; 2866 4209 M (Unconserved)[40 31 25 30 30 26 30 20 25 30 0]xS N 2722 3891 M 2722 3982 I 3025 3982 I 3025 4074 I : 0.996 1 +S K ; : N 3115 3649 485 242 rp C 1 0 scol L ; N 3115 3891 M 3115 3649 I 3600 3649 I 3600 3891 I 3115 3891 I C : 0.996 1 +S K ; 3229 3785 M (Frameshift)[35 20 30 46 30 25 30 11 15 0]xS N 3690 3467 M 3690 3558 I 3358 3558 I 3358 3649 I : 0.996 1 +S K ; : N 3750 3649 485 242 rp C 1 0 scol L ; N 3750 3891 M 3750 3649 I 4235 3649 I 4235 3891 I 3750 3891 I C : 0.996 1 +S K ; 3792 3785 M (Amino Acid Indel)[35 46 10 30 30 15 35 26 10 30 15 15 30 31 30 0]xS N 3690 3467 M 3690 3558 I 3993 3558 I 3993 3649 I : 0.996 1 +S K ; : N 1270 3041 484 243 rp C 1 0 scol L ; N 1270 3284 M 1270 3041 I 1754 3041 I 1754 3284 I 1270 3284 I C : 0.996 1 +S K ; 1306 3145 M (Impacted Protein)[15 45 30 31 25 15 30 30 16 35 20 30 15 30 11 0]xS 1417 3210 M (Domain)[40 30 45 31 10 0]xS N 2843 2922 M 2808 2922 I 2807 2922 I 2806 2921 I 2805 2921 I 2805 2920 I 2805 2919 I 2806 2918 I 2807 2917 I 2808 2917 I 2843 2917 I 2844 2917 I 2845 2918 I 2845 2919 I 2845 2920 I 2845 2921 I 2845 2921 I 2844 2922 I 2843 2922 I 2843 2922 I C 2783 2922 M 2747 2922 I 2746 2922 I 2745 2921 I 2745 2921 I 2745 2920 I 2745 2919 I 2745 2918 I 2746 2917 I 2747 2917 I 2783 2917 I 2783 2917 I 2784 2918 I 2785 2919 I 2785 2920 I 2785 2921 I 2784 2921 I 2783 2922 I 2783 2922 I 2783 2922 I C 2722 2922 M 2687 2922 I 2686 2922 I 2685 2921 I 2684 2921 I 2684 2920 I 2684 2919 I 2685 2918 I 2686 2917 I 2687 2917 I 2722 2917 I 2723 2917 I 2724 2918 I 2724 2919 I 2725 2920 I 2724 2921 I 2724 2921 I 2723 2922 I 2722 2922 I 2722 2922 I C 2662 2922 M 2626 2922 I 2625 2922 I 2625 2921 I 2624 2921 I 2624 2920 I 2624 2919 I 2625 2918 I 2625 2917 I 2626 2917 I 2662 2917 I 2663 2917 I 2663 2918 I 2664 2919 I 2664 2920 I 2664 2921 I 2663 2921 I 2663 2922 I 2662 2922 I 2662 2922 I C 2601 2922 M 2566 2922 I 2565 2922 I 2564 2921 I 2564 2921 I 2563 2920 I 2564 2919 I 2564 2918 I 2565 2917 I 2566 2917 I 2601 2917 I 2602 2917 I 2603 2918 I 2603 2919 I 2604 2920 I 2603 2921 I 2603 2921 I 2602 2922 I 2601 2922 I 2601 2922 I C 2541 2922 M 2505 2922 I 2504 2922 I 2504 2921 I 2503 2921 I 2503 2920 I 2503 2919 I 2504 2918 I 2504 2917 I 2505 2917 I 2541 2917 I 2542 2917 I 2542 2918 I 2543 2919 I 2543 2920 I 2543 2921 I 2542 2921 I 2542 2922 I 2541 2922 I 2541 2922 I C 2481 2922 M 2446 2922 I 2445 2922 I 2444 2921 I 2444 2921 I 2444 2920 I 2444 2919 I 2444 2918 I 2445 2917 I 2446 2917 I 2481 2917 I 2482 2917 I 2483 2918 I 2484 2919 I 2484 2920 I 2484 2921 I 2483 2921 I 2482 2922 I 2481 2922 I 2481 2922 I C 2421 2922 M 2386 2922 I 2385 2922 I 2384 2921 I 2383 2921 I 2383 2920 I 2383 2919 I 2384 2918 I 2385 2917 I 2386 2917 I 2421 2917 I 2422 2917 I 2423 2918 I 2423 2919 I 2423 2920 I 2423 2921 I 2423 2921 I 2422 2922 I 2421 2922 I 2421 2922 I C 2360 2922 M 2325 2922 I 2324 2922 I 2323 2921 I 2323 2921 I 2323 2920 I 2323 2919 I 2323 2918 I 2324 2917 I 2325 2917 I 2360 2917 I 2361 2917 I 2362 2918 I 2363 2919 I 2363 2920 I 2363 2921 I 2362 2921 I 2361 2922 I 2360 2922 I 2360 2922 I C 2300 2922 M 2265 2922 I 2264 2922 I 2263 2921 I 2262 2921 I 2262 2920 I 2262 2919 I 2263 2918 I 2264 2917 I 2265 2917 I 2300 2917 I 2301 2917 I 2302 2918 I 2302 2919 I 2302 2920 I 2302 2921 I 2302 2921 I 2301 2922 I 2300 2922 I 2300 2922 I C 2240 2922 M 2204 2922 I 2203 2922 I 2202 2921 I 2202 2921 I 2202 2920 I 2202 2919 I 2202 2918 I 2203 2917 I 2204 2917 I 2240 2917 I 2240 2917 I 2241 2918 I 2242 2919 I 2242 2920 I 2242 2921 I 2241 2921 I 2240 2922 I 2240 2922 I 2240 2922 I C 2179 2922 M 2144 2922 I 2143 2922 I 2142 2921 I 2141 2921 I 2141 2920 I 2141 2919 I 2142 2918 I 2143 2917 I 2144 2917 I 2179 2917 I 2180 2917 I 2181 2918 I 2181 2919 I 2182 2920 I 2181 2921 I 2181 2921 I 2180 2922 I 2179 2922 I 2179 2922 I C 2119 2922 M 2083 2922 I 2082 2922 I 2082 2921 I 2081 2921 I 2081 2920 I 2081 2919 I 2082 2918 I 2082 2917 I 2083 2917 I 2119 2917 I 2120 2917 I 2120 2918 I 2121 2919 I 2121 2920 I 2121 2921 I 2120 2921 I 2120 2922 I 2119 2922 I 2119 2922 I C 2058 2922 M 2023 2922 I 2022 2922 I 2021 2921 I 2021 2921 I 2020 2920 I 2021 2919 I 2021 2918 I 2022 2917 I 2023 2917 I 2058 2917 I 2059 2917 I 2060 2918 I 2061 2919 I 2061 2920 I 2061 2921 I 2060 2921 I 2059 2922 I 2058 2922 I 2058 2922 I C 1998 2922 M 1963 2922 I 1961 2922 I 1961 2921 I 1960 2921 I 1960 2920 I 1960 2919 I 1961 2918 I 1961 2917 I 1963 2917 I 1998 2917 I 1999 2917 I 1999 2918 I 2000 2919 I 2000 2920 I 2000 2921 I 1999 2921 I 1999 2922 I 1998 2922 I 1998 2922 I C 1937 2922 M 1902 2922 I 1901 2922 I 1900 2921 I 1900 2921 I 1900 2920 I 1900 2919 I 1900 2918 I 1901 2917 I 1902 2917 I 1937 2917 I 1938 2917 I 1939 2918 I 1940 2919 I 1940 2920 I 1940 2921 I 1939 2921 I 1938 2922 I 1937 2922 I 1937 2922 I C 1877 2922 M 1842 2922 I 1841 2922 I 1840 2921 I 1839 2921 I 1839 2920 I 1839 2919 I 1840 2918 I 1841 2917 I 1842 2917 I 1877 2917 I 1878 2917 I 1879 2918 I 1879 2919 I 1879 2920 I 1879 2921 I 1879 2921 I 1878 2922 I 1877 2922 I 1877 2922 I C 1816 2922 M 1781 2922 I 1780 2922 I 1779 2921 I 1779 2921 I 1779 2920 I 1779 2919 I 1779 2918 I 1780 2917 I 1781 2917 I 1816 2917 I 1817 2917 I 1818 2918 I 1819 2919 I 1819 2920 I 1819 2921 I 1818 2921 I 1817 2922 I 1816 2922 I 1816 2922 I C 1756 2922 M 1721 2922 I 1720 2922 I 1719 2921 I 1718 2921 I 1718 2920 I 1718 2919 I 1719 2918 I 1720 2917 I 1721 2917 I 1756 2917 I 1757 2917 I 1758 2918 I 1758 2919 I 1759 2920 I 1758 2921 I 1758 2921 I 1757 2922 I 1756 2922 I 1756 2922 I C 1696 2922 M 1660 2922 I 1659 2922 I 1658 2921 I 1658 2921 I 1658 2920 I 1658 2919 I 1658 2918 I 1659 2917 I 1660 2917 I 1696 2917 I 1696 2917 I 1697 2918 I 1698 2919 I 1698 2920 I 1698 2921 I 1697 2921 I 1696 2922 I 1696 2922 I 1696 2922 I C 1635 2922 M 1600 2922 I 1599 2922 I 1598 2921 I 1598 2921 I 1597 2920 I 1598 2919 I 1598 2918 I 1599 2917 I 1600 2917 I 1635 2917 I 1636 2917 I 1637 2918 I 1637 2919 I 1638 2920 I 1637 2921 I 1637 2921 I 1636 2922 I 1635 2922 I 1635 2922 I C 1575 2922 M 1539 2922 I 1538 2922 I 1538 2921 I 1537 2921 I 1537 2920 I 1537 2919 I 1538 2918 I 1538 2917 I 1539 2917 I 1575 2917 I 1576 2917 I 1576 2918 I 1577 2919 I 1577 2920 I 1577 2921 I 1576 2921 I 1576 2922 I 1575 2922 I 1575 2922 I C 1514 2922 M 1511 2922 I 1514 2920 I 1514 2952 I 1514 2953 I 1513 2954 I 1512 2955 I 1511 2955 I 1510 2955 I 1510 2954 I 1509 2953 I 1509 2952 I 1509 2920 I 1509 2919 I 1510 2918 I 1510 2917 I 1511 2917 I 1514 2917 I 1515 2917 I 1516 2918 I 1517 2919 I 1517 2920 I 1517 2921 I 1516 2921 I 1515 2922 I 1514 2922 I 1514 2922 I C 1514 2977 M 1514 3013 I 1514 3014 I 1513 3014 I 1512 3015 I 1511 3015 I 1510 3015 I 1510 3014 I 1509 3014 I 1509 3013 I 1509 2977 I 1509 2976 I 1510 2976 I 1510 2975 I 1511 2975 I 1512 2975 I 1513 2976 I 1514 2976 I 1514 2977 I 1514 2977 I C 1514 3038 M 1514 3041 I 1514 3042 I 1513 3043 I 1512 3043 I 1511 3043 I 1510 3043 I 1510 3043 I 1509 3042 I 1509 3041 I 1509 3038 I 1509 3037 I 1510 3036 I 1510 3036 I 1511 3035 I 1512 3036 I 1513 3036 I 1514 3037 I 1514 3038 I 1514 3038 I C : L ; : 0.996 1 +S K ; /F1S53 F1 [83 0 0 -83 0 0 ] mFS F1S53 Ji 4247 4324 M ( )S 2015 4395 M (The Classification of SNPs)[51 42 35 21 53 19 34 30 30 19 27 19 35 34 24 20 42 42 21 42 27 21 40 64 48 0]xS 2885 4395 M ( )S 650 4489 M ( )S 650 4583 M (Because of the analysis that may be performed on )[51 35 35 34 41 30 35 21 42 27 21 24 42 35 21 34 42 34 19 35 30 19 30 21 24 42 35 24 21 64 35 35 21 42 35 21 42 35 28 27 42 28 64 35 42 21 42 42 0]xS 2276 4583 M (a SNP varies depending how it may impact the biological )[34 21 40 64 47 21 39 34 28 19 34 30 21 42 35 42 35 42 42 19 42 37 21 43 42 55 21 20 24 21 64 34 35 21 19 64 42 34 35 25 21 24 42 35 21 42 19 42 20 42 37 19 35 34 19 0]xS 650 4677 M (function of the individual, the output may be difficult to parse. Because of this, two files are always produced. ) [27 41 42 35 24 19 42 42 22 42 27 21 24 42 35 21 19 42 42 19 39 19 42 41 34 19 18 21 25 42 35 21 42 41 24 42 41 24 21 64 34 35 21 42 35 21 42 19 27 27 19 35 41 19 24 21 24 42 21 42 34 28 30 36 18 21 21 51 35 35 34 41 30 35 21 42 27 21 24 42 19 30 18 21 25 55 42 21 27 19 19 35 30 21 34 28 35 21 34 19 55 34 35 30 21 42 28 42 42 41 35 35 42 18 21 0]xS 650 4770 M (One that is easy to read, and follows the hierarchy of how it was classified, and th) [65 42 35 21 24 42 34 24 21 19 30 21 35 34 30 35 21 25 42 21 28 35 34 42 18 21 34 42 42 21 27 42 19 19 42 56 30 21 24 42 35 21 42 19 35 28 34 28 35 42 35 21 42 27 21 43 42 55 21 19 24 22 56 34 30 21 35 19 34 30 30 19 27 19 35 42 18 21 34 42 42 21 24 0]xS 3276 4770 M (e other which is easy to parse )[35 21 42 25 42 35 28 21 55 42 19 36 42 21 19 30 21 35 34 30 35 21 24 42 21 42 34 28 30 35 0]xS 650 4864 M (but contains much redundant information between its long lines.) [42 41 24 21 35 42 43 24 34 19 42 30 21 64 41 36 42 21 28 35 42 41 42 42 34 42 24 21 19 42 27 42 28 64 34 24 20 42 42 22 42 35 24 55 35 35 42 21 19 25 30 21 19 43 42 37 21 19 20 43 35 30 0]xS 2740 4864 M ( The normalized output is easy to read and )[21 21 51 42 35 21 42 42 28 64 34 19 20 35 35 42 21 42 41 24 42 42 24 21 19 30 21 35 34 30 35 21 24 42 21 28 35 34 42 21 34 42 42 0]xS 650 4958 M (the denormalized is the easy one to parse. )[24 42 35 21 42 35 42 42 28 64 34 19 19 35 35 42 21 19 30 21 25 42 35 21 35 34 30 35 21 42 43 35 21 24 42 21 42 34 28 30 35 18 21 0]xS 2035 4958 M ( )S F0S96 Ji 650 5210 M (Extracting Coding Information)[106 75 47 52 72 70 47 42 83 81 38 102 78 83 41 83 81 38 59 83 45 78 52 127 72 47 42 78 0]xS 2634 5210 M ( )S F1S64 Ji 650 5360 M (Coding information is extrac)[64 51 50 23 51 45 25 23 51 32 51 33 77 41 29 23 51 51 25 23 36 25 42 46 29 33 41 0]xS 1763 5360 M (ted from the En)[29 42 50 25 32 33 51 77 25 29 51 42 25 66 0]xS 2391 5360 M (sembl database. )[36 42 77 51 23 25 50 41 29 41 51 41 36 42 22 0]xS 3023 5360 M ( )S 650 5473 M ( )S F3S64 Ji 650 5585 M (The format of this extraction is different from the template extraction of Primer Design. Primer design only ) [58 42 29 25 22 35 30 63 41 25 25 35 22 25 25 42 23 29 25 29 50 25 30 41 27 25 23 35 43 25 23 29 25 41 23 22 22 29 30 29 43 25 25 22 30 35 63 25 25 42 29 25 25 29 63 41 21 41 25 29 25 29 50 25 30 41 27 25 23 35 43 25 35 22 25 53 30 23 63 29 30 25 73 29 29 23 32 43 22 25 25 53 30 24 63 29 30 25 41 29 29 23 32 43 25 35 43 22 33 0]xS 650 5698 M (extracts enough information to perform the primer design. SNP analysis, however requires that for a given ) [29 50 25 30 41 27 25 29 25 29 43 35 43 32 42 25 23 43 22 35 30 63 41 25 23 35 43 25 25 35 25 41 29 30 22 35 30 63 25 25 42 29 25 41 30 23 63 29 30 25 41 29 29 23 32 43 22 25 25 49 78 53 25 41 43 41 22 33 29 23 29 22 25 42 35 53 29 34 29 30 25 30 29 43 43 23 30 29 29 26 25 42 41 25 25 22 35 30 25 41 25 32 23 34 29 43 0]xS LH (%%[Page: 4]%%) = %%PageTrailer %%Page: 5 5 %%PageBoundingBox: 12 12 599 779 %%EndPageComments %%BeginPageSetup /DeviceRGB dup setcolorspace /colspABC exch def mysetup concat colspRefresh %%EndPageSetup /DeviceGray dup setcolorspace /colspABC exch def 0 0 scol 650 578 M (region, the entire ge)[30 29 32 23 35 43 22 25 25 42 29 25 29 43 25 23 30 29 25 32 0]xS 1275 578 M (ne is extracted. This is important for computing how an indel or substitution in coding ) [43 29 25 23 29 25 29 50 25 30 41 28 25 29 41 22 25 25 58 42 23 29 25 23 29 25 23 63 41 35 30 25 41 43 25 25 22 35 30 25 27 35 62 41 43 25 23 43 32 25 42 35 53 25 41 43 25 22 43 41 29 22 25 35 30 25 29 43 41 29 25 23 24 43 25 23 35 43 25 23 43 25 27 35 41 23 43 32 0]xS 650 691 M (sequence )[29 29 43 43 29 43 27 29 0]xS 947 691 M (will )[53 23 22 22 0]xS 1092 691 M (affect the result)[41 22 22 29 27 25 25 25 42 29 25 30 29 29 43 22 0]xS 1582 691 M (ant)[41 42 0]xS 1690 691 M ( protein\222s subsequent length.)[25 41 30 35 25 29 23 43 22 29 25 29 43 41 29 29 43 43 29 43 25 25 22 29 43 32 25 42 0]xS 2611 691 M ( )[25 0]xS 2660 691 M ( )S 650 803 M ( )S F1S64 Ji 650 916 M (To extract coding data from the Ensembl database you will first need to know which version ) [61 51 25 42 46 29 33 41 42 29 25 42 51 50 23 51 45 25 50 41 29 41 25 32 33 50 77 25 29 51 42 25 66 51 36 42 77 51 23 25 50 41 29 41 51 41 36 42 25 41 51 49 25 67 23 23 23 25 32 23 33 36 29 25 51 42 42 50 25 29 51 25 47 51 51 67 25 67 51 23 42 51 25 47 42 33 36 23 51 51 0]xS 650 1028 M (and assem)[41 51 50 25 41 36 36 42 0]xS 1049 1028 M (bly of the underlying seque)[51 23 42 25 51 32 25 29 51 42 25 49 51 50 42 33 23 42 23 51 45 25 36 42 49 49 0]xS 2097 1028 M (nce, the template, you are basing your edits )[51 41 42 22 25 29 51 42 25 29 42 77 51 23 40 29 42 22 25 42 51 49 25 41 33 42 25 51 41 36 23 51 45 24 42 51 49 33 25 42 50 22 29 36 0]xS 3788 1028 M (on, and the )[51 51 22 25 41 51 50 25 29 51 42 0]xS 650 1141 M (chromosome and location. )[42 51 33 51 77 51 36 51 77 42 25 41 51 50 25 23 51 42 41 29 23 51 50 22 25 0]xS 1735 1141 M ( Please see the Appendix on how to determine which assembly )[25 56 23 42 41 36 42 25 36 42 42 25 29 51 42 25 68 51 51 42 51 49 22 46 25 51 51 25 51 51 67 25 29 51 25 50 42 29 42 33 77 23 51 42 25 66 51 23 42 51 25 41 36 36 42 77 51 23 42 0]xS 650 1253 M (and annotation builds are available at a particular instance of time. ) [41 51 50 25 41 51 51 51 29 41 29 23 51 51 25 51 49 23 23 50 36 25 41 33 42 24 41 47 41 23 23 41 50 23 42 25 41 29 25 41 25 50 41 33 29 23 42 49 23 41 33 25 23 51 36 29 41 51 42 42 25 51 32 25 29 23 77 42 22 25 0]xS 3254 1253 M ( )S 650 1366 M ( )S 650 1478 M (There are two)[61 51 42 33 42 25 41 33 42 25 29 67 0]xS 1192 1478 M ( programs that are available for extracting coding information. One is by a ) [25 51 33 51 45 33 41 77 36 25 30 51 41 29 25 41 33 42 25 41 47 40 23 23 41 51 23 42 25 32 51 33 25 42 46 29 33 41 41 29 23 51 45 25 42 51 50 23 51 45 25 23 51 32 51 33 77 41 29 23 51 51 22 25 25 78 51 42 25 23 36 25 51 42 25 41 0]xS 650 1591 M (single template, and the other is by batch. )[36 23 51 45 23 42 25 29 42 77 51 23 41 29 42 22 25 41 51 50 25 29 50 42 25 51 29 51 42 33 25 23 36 25 51 42 25 51 41 29 42 51 22 25 0]xS F3S64 Ji 2308 1591 M (When you are using output from Primer Design as a basis )[89 42 29 43 25 33 35 43 24 41 30 29 25 43 29 23 43 32 25 35 43 25 41 43 25 25 22 30 35 63 25 53 30 23 63 29 30 24 73 29 29 23 32 43 25 41 29 25 41 25 41 41 29 23 29 0]xS 650 1703 M (for your template, you will want to use the batch extraction approach.) [22 35 30 25 33 35 43 30 25 25 29 63 41 22 41 25 29 22 25 33 35 43 25 53 23 22 22 25 53 41 43 25 25 25 35 25 43 29 29 25 25 42 29 25 41 41 25 27 42 25 29 50 25 30 41 27 25 23 35 43 25 41 40 41 30 35 41 27 42 0]xS 2923 1703 M ( When e)[25 25 89 42 29 43 25 0]xS 3230 1703 M (xtracting data for a Primer )[50 25 30 41 27 25 22 43 32 25 41 41 25 40 25 22 35 30 25 41 25 53 30 23 63 29 30 0]xS 650 1816 M (Design run you have two options. 1.\) You can extract both the template and coding information data at the ) [73 29 29 23 32 43 25 30 43 43 25 33 35 43 25 42 41 34 29 25 25 53 35 25 35 41 25 23 36 43 29 22 25 25 47 22 27 25 25 65 35 43 25 27 41 43 25 29 50 25 30 41 27 25 25 41 35 25 42 24 25 42 29 25 25 29 63 41 22 41 25 29 24 41 43 41 25 27 35 41 23 43 32 25 22 43 22 35 30 62 41 25 23 35 43 25 41 41 25 41 24 41 25 25 25 42 29 0]xS 650 1928 M (same time to ensure that your assembly and build are the same) [29 41 63 29 25 25 23 63 29 25 25 35 25 29 43 29 43 30 29 25 25 42 41 25 25 33 35 43 30 25 41 29 29 29 63 41 22 33 25 41 42 41 25 41 43 23 21 41 25 41 30 29 25 25 42 29 25 29 40 63 0]xS 2701 1928 M ( between primer design and SNP analysis)[25 41 29 25 53 29 29 43 25 41 30 23 63 29 30 25 41 29 29 23 32 43 25 40 43 41 24 50 78 53 25 41 43 41 22 33 29 23 0]xS 4078 1928 M (, )[22 0]xS 650 2041 M (since once old ver)[29 23 43 27 29 25 35 43 27 29 25 35 22 41 25 34 29 0]xS 1201 2041 M (sions)[29 24 35 43 0]xS 1361 2041 M ( may)[25 63 41 0]xS 1523 2041 M ( go offline )[25 32 35 26 35 22 22 22 23 43 29 0]xS 1862 2041 M (and )[41 43 41 0]xS 2012 2041 M (no longer be)[43 35 25 22 35 43 32 29 30 25 41 0]xS 2401 2041 M (come available)[27 35 63 29 25 41 34 41 23 22 41 41 22 0]xS 2874 2041 M (, or 2.\) You can extract the coding )[22 25 35 30 25 47 22 27 25 65 35 43 25 27 40 43 25 29 50 25 30 41 27 24 25 25 42 29 25 27 35 41 23 43 32 0]xS 650 2153 M (information at a later time, and use the amplicon mapping scripts to convert the old assembly positions to new ) [23 43 22 35 30 63 41 25 23 35 43 25 41 25 25 41 24 22 41 25 29 30 25 25 23 63 29 22 25 40 42 41 25 43 29 29 25 25 42 29 25 41 62 41 22 23 27 35 43 25 62 41 41 41 22 43 32 25 29 27 30 23 41 25 29 25 25 35 25 27 35 43 34 29 30 25 25 25 42 29 26 35 22 41 25 41 29 29 29 63 41 21 33 25 41 35 29 23 25 23 35 43 29 25 25 35 25 43 29 53 0]xS 650 2266 M (positions)[41 35 29 23 25 23 35 43 0]xS 933 2266 M ( in order)[25 23 43 25 35 30 41 29 0]xS 1214 2266 M ( to take advantage of the latest )[25 25 35 25 25 41 52 29 25 41 41 34 41 43 25 41 32 29 25 35 22 25 25 42 29 25 22 41 25 29 29 25 0]xS 2247 2266 M (annotat)[41 43 43 35 25 41 0]xS 2500 2266 M (ion publicly available. Chances are that if your )[23 35 43 24 40 43 41 22 23 27 22 33 25 41 34 41 23 22 40 41 22 29 22 25 25 62 42 41 43 27 29 29 25 41 30 29 24 25 42 41 25 25 23 22 25 33 35 43 30 0]xS 650 2378 M (amplicon )[41 63 41 22 23 27 35 43 0]xS 969 2378 M (does)[41 35 29 0]xS 1103 2378 M ( not be mapped to the new assembly,)[25 43 35 25 25 41 29 25 63 41 40 41 29 41 25 24 35 25 25 42 29 25 43 29 53 25 41 29 29 29 63 41 22 33 0]xS 2295 2378 M ( that)[25 25 42 41 0]xS 2453 2378 M ( the amplicon or annotation is wrong. )[25 24 42 29 25 40 63 41 22 23 27 35 43 25 35 30 25 41 43 43 35 25 41 25 23 35 43 25 23 29 25 53 30 35 43 32 22 25 0]xS 3728 2378 M ( )S /F0S75 F0 [117 0 0 -117 0 0 ] mFS F0S75 Ji 650 2605 M (Single Region Extraction)[60 33 65 63 30 55 29 81 55 63 33 61 65 28 83 58 37 40 55 55 37 33 60 0]xS 1894 2605 M ( )S F1S64 Ji 650 2747 M (Coding information is extracted with the following script:)[64 51 50 23 51 45 25 23 51 32 51 33 77 41 29 23 51 51 25 23 36 25 42 46 29 33 41 42 29 42 50 25 67 23 29 51 25 29 51 42 25 32 51 23 23 51 67 23 51 45 24 36 42 33 23 51 29 0]xS 2877 2747 M ( )S 650 2859 M ( )S %%IncludeResource: font Courier 7500 VM? /Courier FontHasEuro not { /Euro.Courier [600 0 17 -12 578 584 ] <9CF8EC0DD1C303F88DC1037FC201F760C201F7CEC201F8A5C201F76004DB06A8FB0FE32E F7278B08DA8BD8A8C8B80873BA0556644870478B08278B39C56DF208F776069FC205FB94 068B968A968B96088B928B938C9208F7A6069FC205FBB106A3EAD3CCEB8B08D18BD071B1 63084307C106F75507550656075AAE569D438B08FB188B2D2D70FB0D085106775405D106 7A078B7E8C7F8C7E085706090E> AddEuroGlyph /Euro /Courier /Courier-Copy BuildNewFont } if F /F6 0 /256 T /Courier mF /F6S53 F6 [83 0 0 -83 0 0 ] mFS F6S53 Ji 650 2957 M (Extract_Coding_Info.pl)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1750 2957 M ( )S 650 3051 M ( )[50 50 50 50 0]xS 900 3051 M ( [required])[50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1550 3051 M ( )S 650 3146 M ( )[50 50 50 50 50 50 50 0]xS 1050 3146 M (-)S 1100 3146 M (c chromosome)[50 50 50 50 50 50 50 50 50 50 50 0]xS 1700 3146 M ( )S 650 3240 M ( )[50 50 50 50 50 50 50 0]xS 1050 3240 M (-)S 1100 3240 M (b begin \(absolute ensemble 1)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2500 3240 M (-)S 2550 3240 M (residue based coordinates\))[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3850 3240 M ( )S 650 3334 M ( )[50 50 50 50 50 50 50 0]xS 1050 3334 M (-)S 1100 3334 M (e end \(absolute ensemble 1)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2400 3334 M (-)S 2450 3334 M (residue based coordinates\))[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3750 3334 M ( )S 650 3429 M ( )S 650 3523 M ( )[50 50 50 50 50 50 50 0]xS 1050 3523 M (-)S 1100 3523 M (O "", for example "homo sapiens")[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3200 3523 M ( )S 650 3618 M ( )[50 50 50 50 50 50 50 0]xS 1050 3618 M (-)S 1100 3618 M (B , for ex)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2600 3618 M (ample 21)[50 50 50 50 50 50 50 0]xS 3000 3618 M ( )S 650 3712 M ( )[50 50 50 50 50 50 50 0]xS 1050 3712 M (-)S 1100 3712 M (A , for example 34d)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3200 3712 M ( )S 650 3806 M ( )S 650 3901 M ( [optional])[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1550 3901 M ( )S 650 3995 M ( )[50 50 50 50 50 50 50 0]xS 1050 3995 M (-)S 1100 3995 M (x automatically expand extraction range to include)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3600 3995 M ( )S 650 4090 M ( all the exons overlapping the range specified.) [50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3750 4090 M ( )S 650 4184 M ( )[50 50 50 50 50 50 50 0]xS 1050 4184 M (-)S 1100 4184 M (f preferred output filename)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2450 4184 M ( )S F1S64 Ji 650 4293 M ( )S 650 4406 M (If you want th)[35 32 25 42 51 49 25 67 41 51 29 25 29 0]xS 1202 4406 M (e protein predictions for a given SNP to be computed properly, the ) [42 25 51 33 51 29 42 23 51 25 51 33 42 50 23 42 29 23 51 51 36 25 32 51 33 25 41 25 45 23 47 42 51 25 48 77 56 25 29 51 25 51 42 25 42 51 77 51 49 29 42 50 25 51 33 51 51 42 33 23 42 22 24 29 51 42 0]xS 3834 4406 M <96>S 3884 4406 M (x option )[46 25 51 51 29 23 51 51 0]xS 650 4518 M (should be specified. )[36 51 51 49 23 50 25 51 42 25 36 51 42 42 23 32 23 42 50 22 25 0]xS 1466 4518 M (If the preferred output filename is not specified, the default filename) [35 32 25 29 51 42 25 51 33 42 32 42 33 33 42 50 25 51 49 29 51 49 29 25 32 23 23 42 51 41 77 42 25 23 36 25 51 51 29 25 36 51 42 42 23 32 23 42 50 22 25 29 51 42 25 50 42 32 40 49 23 29 25 32 23 23 42 51 41 77 0]xS 4123 4518 M ( )S 650 4631 M (prefixes)[51 33 42 32 23 46 42 0]xS 955 4631 M ( will be .)[77 51 36 51 77 42 67 22 67 51 41 45 23 51 0]xS 2271 4631 M (-)S 2302 4631 M (.)[67 42 51 49 67 0]xS 2600 4631 M ( )S %%IncludeResource: font Garamond-KursivHalbfett 7500 VM? /Garamond-KursivHalbfett FontHasEuro not { /Euro.Garamond-KursivHalbfett [500 0 9 -20 542 686 ] <94F8880DD6F70503F815A503F86FAB037DA801F78FC801F805C801F922A8018F0AD6F705 03F815A503F86FAB037DA801F78FC801F805C801F898F72401F8A9F942157306867E857E 7F8B088F0AD6F70503F815A503F86FAB037DA801F78FC801F805C801F922A801778B79A2 428B08288BFB07285BFB2E084B06734E05D206877C8271897B085306724E05D8068A7E8A 7C8B7B082CACFB12F72F1EC18BA2A2AB8B088F0AD6F70503F815A503F86FAB038C7601F7 8FC801F805C801F922A801978B8B788C8108A5068F0AD6F70503F815A503F86FAB0394F7 1F01F78FC801F805C801F922A801B4F73C056B068F0AD6F70503F815A503F86FAB037DA8 01F78FC801F805C801F922A8017E64552D458B084A6DB3D41F8BAD92B497BB08F73606A3 C805FB43068D9892AA909808F74C06A4C805FB57068D9092A295A908A3D4B2E8C48B08B6 BA6A301F8F0AD6F70503F815A503F86FAB037DA801F78FC801F805C801F898F724017D07 AB06090E> AddEuroGlyph /Euro /Garamond-KursivHalbfett /Garamond-KursivHalbfett-Copy BuildNewFont } if F /F7 0 /256 T /Garamond-KursivHalbfett mF /F7S75 F7 [117 0 0 -117 0 0 ] mFS F7S75 Ji 650 4857 M (Batched Regions Extraction)[76 57 34 39 62 46 59 29 79 46 52 34 55 61 41 29 76 66 34 40 57 39 34 34 55 0]xS 1945 4857 M ( )S %%IncludeResource: font Courier-Oblique 7500 VM? /Courier-Oblique FontHasEuro not { /Euro.Courier-Oblique /Courier-Oblique UseObliqueEuro { [600 0 51 -12 677 583 ] } { [600 0 17 -12 578 584 ] <9CF8EC0DD1C303F88DC1037FC201F760C201F7CEC201F8A5C201F76004DB06A8FB0FE32E F7278B08DA8BD8A8C8B80873BA0556644870478B08278B39C56DF208F776069FC205FB94 068B968A968B96088B928B938C9208F7A6069FC205FBB106A3EAD3CCEB8B08D18BD071B1 63084307C106F75507550656075AAE569D438B08FB188B2D2D70FB0D085106775405D106 7A078B7E8C7F8C7E085706090E> } ifelse AddEuroGlyph /Euro /Courier-Oblique /Courier-Oblique-Copy BuildNewFont } if F /F8 0 /256 T /Courier-Oblique mF /F8S53 F8 [83 0 0 -83 0 0 ] mFS F8S53 Ji 650 4986 M (Extract_Codin)[50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1300 4986 M (g_Info_by_Batch.pl)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2200 4986 M ( )S 650 5080 M ( [required])[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1550 5080 M ( )S 650 5174 M ( )[50 50 50 50 50 50 50 0]xS 1050 5174 M (-)S 1100 5174 M (l Target List)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2000 5174 M ( )S 650 5269 M ( )[50 50 50 50 50 50 50 0]xS 1050 5269 M (-)S 1100 5269 M (t Template Directory)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2350 5269 M ( )S 650 5363 M ( )[50 50 50 50 50 50 50 0]xS 1050 5363 M (-)S 1100 5363 M (o Coding Info Output Directory)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2850 5363 M ( )S 650 5458 M ( )S 650 5552 M ( [optional])[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1550 5552 M ( )S 650 5646 M ( )[50 50 50 50 50 50 50 0]xS 1050 5646 M (-)S 1100 5646 M (B Build \(override build in .dat file\))[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3200 5646 M ( )S 650 5741 M ( )[50 50 50 50 50 50 50 0]xS 1050 5741 M (-)S 1100 5741 M (A Assembly \(override ass)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2550 5741 M (embly in .dat file\))[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3500 5741 M ( )S 650 5835 M ( )S LH (%%[Page: 5]%%) = %%PageTrailer %%Page: 6 6 %%PageBoundingBox: 12 12 599 779 %%EndPageComments %%BeginPageSetup /DeviceRGB dup setcolorspace /colspABC exch def mysetup concat colspRefresh %%EndPageSetup /DeviceGray dup setcolorspace /colspABC exch def 0 0 scol F3S64 Ji 650 578 M (This program will extract the necessary coding information for a given list of targets based on the build and ) [58 42 23 29 25 41 30 35 32 30 41 63 25 53 23 22 22 25 29 50 25 30 41 27 25 25 25 42 29 25 43 29 27 29 29 29 41 30 33 25 27 35 41 23 43 32 25 23 43 22 35 30 63 41 25 23 35 43 25 22 35 30 25 41 25 32 23 34 29 43 25 22 23 29 25 25 35 22 25 25 41 30 32 29 25 29 25 41 41 29 29 41 25 36 43 25 25 42 29 25 41 43 23 21 41 25 41 42 41 0]xS 650 691 M (assembly of the )[41 29 29 29 63 41 22 33 25 35 22 25 25 42 29 0]xS 1165 691 M (template )[25 29 63 41 21 41 25 29 0]xS 1464 691 M (extraction.)[29 50 25 30 41 27 25 23 35 43 0]xS 1814 691 M ( Th)[25 25 58 0]xS 1964 691 M (is batch extraction uses the .dat file, which contains the build and ) [23 29 25 41 41 25 27 42 25 29 50 25 30 41 27 25 23 35 43 25 43 28 29 29 25 25 42 29 25 22 41 41 25 25 22 23 22 29 22 25 53 42 23 26 42 25 27 35 43 25 41 23 43 29 24 25 42 29 25 41 43 23 22 41 24 41 43 41 0]xS 650 803 M (assembly version)[41 29 29 29 63 41 22 33 25 34 29 30 29 23 35 0]xS 1185 803 M ( of the template used in primer design as a basis for extracting the coding information ) [25 35 22 25 25 42 29 25 25 29 63 41 22 41 24 29 25 43 29 29 41 25 23 43 25 41 30 23 63 29 30 25 41 29 29 23 32 43 25 41 29 24 41 25 41 40 29 23 29 25 22 35 30 25 29 50 25 30 41 27 25 23 43 32 25 25 42 29 25 27 35 41 23 43 32 25 23 43 22 35 30 63 41 25 23 35 43 0]xS 650 916 M (necessary for SNP classification. As mentioned before, this script will by default extend the feature ) [43 29 27 29 29 29 41 30 33 25 22 35 30 25 50 78 53 26 27 22 41 29 29 23 22 23 27 41 25 23 35 43 22 25 25 76 29 25 63 29 43 25 23 35 43 29 41 25 41 29 22 35 30 29 22 25 25 42 23 29 25 28 27 30 23 41 25 25 53 23 22 22 25 41 33 25 41 29 22 41 43 22 25 25 29 50 25 29 42 41 25 25 42 28 25 22 29 41 25 43 30 29 0]xS 650 1028 M (extraction range to include the entire gene so that )[29 50 25 30 41 27 25 23 35 43 25 30 41 43 32 29 25 25 35 25 23 43 27 22 43 41 29 25 25 42 29 25 29 43 25 23 30 29 25 32 29 43 29 25 29 35 25 25 42 41 25 0]xS 2271 1028 M (a modified )[41 25 63 35 41 23 22 23 29 41 0]xS 2639 1028 M (pr)[40 0]xS 2709 1028 M (otein sequence can be properly predicted. If the )[35 25 29 23 43 25 29 29 43 43 29 43 27 29 25 27 41 43 25 41 29 25 41 30 35 41 29 30 22 33 25 41 30 29 41 23 27 25 29 41 22 25 25 32 22 25 25 42 29 0]xS 650 1141 M (build/assembly that was used for primer design is no longer available in Ensembl, then it will be necessary to ) [41 43 23 22 41 49 41 29 29 29 63 41 22 33 25 25 42 41 25 25 52 41 29 25 43 29 29 41 24 22 35 30 25 41 30 23 63 29 30 25 41 29 29 23 32 43 25 23 29 25 43 35 25 22 35 43 32 29 30 25 41 34 41 23 22 41 41 22 29 25 23 43 24 69 43 29 29 63 41 21 22 25 25 42 29 43 25 23 25 25 53 22 22 22 25 41 29 25 43 29 27 29 29 29 41 30 33 25 25 35 0]xS 650 1253 M (specify an overriding build and assembly and run the amplicon mapping script) [29 41 29 27 23 22 33 25 41 43 25 35 34 29 30 30 23 41 23 43 32 25 41 43 23 22 41 25 40 43 40 25 41 29 29 29 63 41 22 33 25 41 42 41 25 30 43 43 25 25 42 29 25 40 63 41 21 23 27 35 43 25 63 40 41 41 23 43 32 25 29 27 30 23 41 0]xS 3200 1253 M (s for coordinate co)[29 25 22 35 30 25 27 35 35 30 41 23 43 41 25 29 25 27 0]xS 3782 1253 M (mpatibility)[63 41 41 25 23 41 23 22 23 25 0]xS 4142 1253 M (. )[22 25 0]xS 4214 1253 M ( )S F0S96 Ji 650 1509 M (Classifying SNPs)[102 39 72 62 62 42 45 70 42 84 81 38 77 126 92 0]xS 1746 1509 M ( )S F1S64 Ji 650 1659 M (The SNP Classifier is capable of annotating a SNP given its allele, orientation, and position. ) [61 51 42 25 48 77 56 25 64 23 41 36 36 23 32 23 42 33 25 23 36 25 42 41 51 41 51 23 42 25 51 32 25 41 51 51 51 29 41 29 23 51 45 25 41 25 48 77 56 25 44 23 47 42 51 25 23 29 36 25 41 23 23 42 23 42 22 25 51 33 22 42 51 29 41 29 23 51 51 22 24 41 51 50 25 51 51 36 23 29 23 51 51 22 25 0]xS 650 1772 M (The allele should be one of A, T, C, or G, or the null or delete character, the hyphen \(\223) [61 51 42 25 41 23 23 42 23 42 25 36 51 51 49 23 50 25 51 42 25 51 51 42 25 50 32 25 68 22 25 61 22 25 64 22 25 51 33 25 77 22 25 51 33 25 29 51 42 25 51 49 23 23 25 51 33 25 50 42 23 42 29 42 25 42 51 41 33 40 42 29 42 33 22 25 29 51 42 25 50 42 51 51 42 51 25 29 0]xS 4016 1772 M (-)S 4047 1772 M (\223\). )[45 29 22 25 0]xS 650 1884 M (Ambiguity codes will not generate)[68 77 51 23 45 49 23 29 42 25 42 51 50 42 36 25 67 23 22 23 25 51 51 29 25 45 42 51 42 33 41 29 0]xS 1969 1884 M ( proper protein predictions, so it is useful to use the actual ) [25 51 33 51 51 42 33 25 51 33 51 29 42 23 51 25 51 33 42 50 23 42 29 23 51 51 36 22 25 36 51 25 23 29 25 23 36 25 49 36 42 32 49 23 25 30 51 25 49 36 42 25 29 51 42 25 41 42 29 49 41 23 0]xS 650 1997 M (alleles when possible.)[41 23 23 42 23 42 36 25 67 50 42 51 25 51 51 36 36 23 51 23 42 0]xS 1475 1997 M ( )S F0S75 Ji 650 2223 M (Alleles Input File)[77 30 30 55 30 55 49 29 46 65 64 65 37 29 71 33 30 0]xS 1500 2223 M ( )S F1S64 Ji 650 2366 M (The input file that the SNP Classifier needs consists of begin, end, orientation and allele. ) [61 51 42 25 23 51 51 49 29 25 32 23 23 42 25 29 51 41 29 25 29 51 42 25 48 77 56 25 64 23 41 36 36 23 32 23 42 33 25 51 42 42 50 36 25 42 51 51 36 23 36 29 37 25 51 32 25 51 42 45 23 51 22 25 42 51 50 22 25 51 33 23 42 51 29 41 29 23 51 50 25 41 51 50 25 41 23 23 42 22 42 22 25 0]xS 650 2478 M (The begin and end are in 0)[61 51 42 25 51 42 45 23 51 25 41 51 50 25 42 51 50 25 41 33 42 24 23 51 24 0]xS 1686 2478 M (-)S 1717 2478 M (space based coordinates. )[36 51 41 42 42 25 51 41 36 42 50 25 42 51 51 33 50 23 51 41 29 42 35 22 25 0]xS F3S64 Ji 2719 2478 M (It)[32 0]xS 2776 2478 M ( i)[25 0]xS 2824 2478 M (s)S 2853 2478 M ( based on the simple regions file used in )[25 41 41 29 29 41 25 35 43 25 25 42 29 25 29 23 63 40 22 29 25 30 29 32 23 35 43 29 25 22 23 22 29 25 43 29 29 41 25 23 43 0]xS 650 2591 M (primer design, where the allele is considered )[41 30 23 63 29 30 25 41 29 29 23 32 43 22 25 53 42 29 30 29 25 25 42 29 25 41 22 22 29 22 29 24 23 29 25 27 35 43 29 23 41 29 30 29 41 0]xS 2082 2591 M (a )[41 0]xS 2148 2591 M (comment.)[27 35 63 63 29 43 25 0]xS 2455 2591 M ( )S 650 2703 M ( )S F1S64 Ji 650 2816 M (The Backus)[61 51 42 25 61 41 42 47 49 0]xS 1105 2816 M (-)S 1136 2816 M (Normal Form for this file is:)[77 51 33 77 41 23 25 56 51 34 77 25 32 51 33 25 29 51 23 36 26 32 23 23 42 25 23 36 0]xS 2238 2816 M ( )S F1S53 Ji 650 2913 M (<)S 705 2913 M (edit )[35 42 19 24 0]xS 846 2913 M (list> ::= <)[19 19 30 25 55 21 18 18 55 22 0]xS 1183 2913 M (edit)[35 42 19 0]xS 1303 2913 M ( list> <)[21 19 19 30 25 55 21 0]xS 1548 2913 M (edit )[35 42 19 25 0]xS 1690 2913 M (record> | )[28 35 35 42 28 42 55 21 42 0]xS /F3S53 F3 [83 0 0 -83 0 0 ] mFS F3S53 Ji 2039 2913 M (NULL)[65 60 53 0]xS F1S53 Ji 2270 2913 M ( )S 650 3007 M (<)S 705 3007 M (edit)[35 42 19 0]xS 825 3007 M ( record> ::= )[21 28 35 35 42 28 42 55 21 18 18 55 21 55 28 35 37 20 42 43 55 0]xS 1580 3007 M <93>S 1617 3007 M (\\)S 1659 3007 M (t\224 )[24 37 0]xS 1741 3007 M (<)S 1796 3007 M (allele list)[34 19 19 35 19 35 21 19 19 30 0]xS 2071 3007 M (> \223)[55 21 0]xS 2184 3007 M (\\)S 2226 3007 M <6E94>[42 0]xS 2305 3007 M ( )S 650 3101 M ( ::= <)[55 28 35 37 19 43 42 55 21 18 19 55 21 0]xS 1154 3101 M (begin> \223)[42 35 37 19 43 55 21 0]xS 1443 3101 M (\\)S 1485 3101 M (t\224 \223)[24 37 22 55 36 42 42 55 21 0]xS 1856 3101 M (\\)S 1898 3101 M (t\224 )[24 37 22 55 42 28 19 35 42 24 35 24 19 43 42 0]xS 2444 3101 M ( )S 650 3209 M ( ::= )[55 42 35 37 20 42 55 21 19 18 55 0]xS F3S64 Ji 1070 3209 M (integer)[23 43 25 29 32 29 0]xS F1S53 Ji 1281 3209 M ( )S 650 3322 M ( ::= )[55 35 42 42 55 21 18 19 55 0]xS F3S64 Ji 1013 3322 M (integer)[23 43 25 29 32 29 0]xS F1S53 Ji 1224 3322 M ( )S 650 3419 M ( ::= 1 | )[55 42 28 19 35 42 24 35 24 19 43 42 55 21 19 18 55 21 39 21 42 0]xS 1370 3419 M (-)S 1396 3419 M (1)S 1435 3419 M ( | 0)[21 42 21 0]xS F3S53 Ji 1558 3419 M ( )S F1S53 Ji 650 3513 M (<)S 705 3513 M (allele list)[34 19 19 35 19 35 21 19 19 30 0]xS 979 3513 M (> ::= )[55 21 19 18 55 0]xS 1169 3513 M ( | )[55 34 19 19 35 19 35 55 21 42 0]xS 1524 3513 M ()[55 34 19 20 35 19 35 21 19 19 30 24 0]xS 1909 3513 M ( \223/\224 )[21 37 42 37 21 55 34 19 19 35 19 35 0]xS 2338 3513 M ( )S 650 3607 M ( ::= \223C\224 | \223A\224 | \223T\224)[55 34 19 19 35 19 35 55 21 18 18 55 22 37 53 37 55 34 19 19 35 19 36 55 21 42 21 37 56 38 55 34 19 19 35 19 35 55 21 42 21 37 51 0]xS 2149 3607 M ( )S 2170 3607 M ( | \223G\224)[55 34 19 19 35 19 35 55 21 42 21 37 65 0]xS 2664 3607 M ( )S 2685 3607 M ( | \223)[55 34 19 19 35 19 35 55 21 42 21 0]xS 3077 3607 M (-)S 3103 3607 M (\223 | NULL)[37 55 34 19 19 35 19 35 55 21 42 21 64 59 49 0]xS F1S64 Ji 3715 3607 M ( )S 650 3716 M ( )S 650 3828 M (An ex)[68 51 25 42 0]xS 882 3828 M (ample of an alleles input file would be:)[41 77 51 23 42 25 51 32 25 41 51 24 41 23 23 42 22 42 36 25 23 51 51 49 29 25 32 23 23 42 25 67 51 49 23 50 25 51 42 0]xS 2372 3828 M ( )S F6S53 Ji 650 3926 M (367445 367446 1 C/G)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2000 3926 M ( )S 650 4020 M (369615 369616 1 T)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1900 4020 M ( )S 650 4114 M (369709 369710 1 A/G)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2000 4114 M ( )S 650 4209 M (385689 385690 1 A/G)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2000 4209 M ( )S 650 4303 M (385898 385899 1 A)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1900 4303 M ( )S 650 4398 M (386128 386129 1 A/G)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2000 4398 M ( )S 650 4492 M (404563 404564 1 T/C)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2000 4492 M ( )S F1S64 Ji 650 4601 M ( )S 650 4714 M (Note that since the )[77 51 29 42 25 29 51 41 29 25 36 23 51 42 42 25 29 51 42 0]xS 1415 4714 M (be)[51 0]xS 1508 4714 M (ginning)[45 23 50 51 23 51 0]xS 1796 4714 M ( and end)[25 41 51 50 25 42 51 0]xS 2131 4714 M (ing)[23 51 0]xS 2250 4714 M ( positions)[25 51 51 36 23 29 23 51 51 0]xS 2626 4714 M ( are in space base coordinates, the )[25 41 33 42 25 23 51 25 36 51 41 42 42 25 51 41 36 42 24 42 51 51 33 50 23 51 41 29 42 36 22 25 29 51 42 0]xS 3965 4714 M (region )[33 42 45 23 51 51 0]xS 650 4826 M (between the two values will represent which nucleotides are impacted on the reference ) [51 42 29 67 42 42 51 25 29 51 42 25 28 67 51 25 47 41 23 49 42 36 25 67 22 23 23 25 33 42 51 33 42 36 42 51 29 25 67 51 23 42 51 25 51 49 42 23 42 51 29 22 50 42 36 25 41 33 42 25 23 77 51 41 42 29 42 50 25 51 51 25 29 51 42 25 33 41 32 42 33 42 51 42 42 0]xS 650 4939 M (sequence. So if the difference between the begin)[36 42 49 49 42 51 42 42 22 25 25 48 51 25 23 32 25 29 51 42 25 50 23 32 32 42 32 42 51 42 42 25 51 42 28 67 42 42 51 25 29 51 42 25 50 42 45 23 0]xS 2545 4939 M (ning)[51 22 51 0]xS 2714 4939 M ( and the end)[25 41 51 50 25 29 51 42 25 42 51 0]xS 3196 4939 M (ing)[23 51 0]xS 3315 4939 M ( are 3 bp and the allele\222s )[24 41 33 42 25 47 25 50 51 25 41 51 50 25 29 51 42 25 41 23 23 42 22 42 22 36 0]xS 650 5051 M (leng)[23 42 51 0]xS 811 5051 M (th is not equal to 3, then you will by definition an )[29 51 25 23 36 25 51 51 29 25 42 49 49 41 23 25 29 51 25 47 22 25 29 50 42 51 25 42 51 49 25 67 23 23 23 25 50 42 25 50 42 32 23 51 23 29 23 51 51 25 40 51 0]xS 2742 5051 M (have )[51 41 47 42 0]xS 2948 5051 M (indel. Otherwise, the edit will be )[23 51 50 42 23 22 25 25 25 78 29 51 42 33 66 23 36 42 22 24 29 51 42 25 42 50 23 29 25 67 23 23 23 25 51 42 0]xS 650 5164 M (a )[41 0]xS 716 5164 M (simple )[36 23 77 51 23 42 0]xS 993 5164 M (substitution.)[36 49 51 36 29 23 29 49 29 23 51 51 0]xS 1471 5164 M ( The beginning and ending positions of the edit must also be with ) [25 25 61 52 42 25 51 42 45 23 51 51 23 51 45 24 41 51 50 25 42 51 50 23 51 45 25 50 51 36 23 29 23 51 51 36 25 51 32 25 29 51 42 25 42 50 23 29 25 77 49 37 29 25 41 23 36 51 25 51 42 25 67 23 29 51 0]xS 650 5276 M (respect to the 0 position of the coding information that was extracted. ) [33 42 36 51 42 42 29 25 29 51 25 29 51 42 25 47 25 51 51 36 23 29 23 51 51 25 51 32 25 29 51 42 25 42 51 50 23 51 45 25 23 51 32 51 33 77 41 29 23 51 51 25 29 51 41 29 25 67 41 36 25 42 46 29 33 41 42 29 42 50 22 0]xS 3388 5276 M ( In other words, )[25 35 51 25 51 29 50 42 33 25 67 51 33 50 36 22 0]xS 650 5389 M (absolute genomic coordinates will not work, unless your coding information happens to be ) [41 51 36 51 23 49 29 42 25 45 42 51 51 77 23 42 25 42 51 51 33 50 23 50 41 29 42 36 25 67 23 23 23 25 51 51 29 25 67 51 33 47 22 25 49 51 23 42 36 36 25 42 51 49 33 25 42 51 50 23 51 45 25 23 51 32 51 33 77 41 29 23 51 51 25 51 41 51 51 42 51 36 25 29 51 25 51 42 0]xS 650 5501 M (extracted from the beginning of the chromosome!)[42 46 29 33 41 42 29 42 50 25 32 33 51 77 25 29 51 42 25 51 42 45 23 51 50 23 51 45 25 51 32 25 29 51 42 25 42 51 33 51 77 51 36 51 77 42 0]xS 2588 5501 M ( )S 650 5614 M ( )S F3S64 Ji 650 5726 M (In general, the orientation coming from )[32 43 25 32 29 43 29 30 41 22 22 25 25 42 29 25 35 30 23 29 43 25 41 25 23 35 43 25 27 35 63 23 43 32 25 22 30 35 63 0]xS 1944 5726 M (our )[35 43 30 0]xS 2077 5726 M (trace processing will be 1, because the primers are desig)[25 30 41 27 29 25 41 30 35 27 29 29 29 23 43 32 25 53 24 22 22 25 41 29 25 47 22 25 41 29 27 41 43 29 29 25 24 42 29 25 41 30 23 63 29 30 29 25 41 30 28 25 41 29 29 23 0]xS 3864 5726 M (ned in the )[43 29 41 25 23 43 25 25 42 29 0]xS 650 5839 M (orientation of)[35 30 23 29 43 25 41 25 23 35 43 25 35 0]xS 1084 5839 M ( the)[25 25 42 0]xS 1205 5839 M ( reference genome. In other assays, for example where cDNA or ESTs) [25 30 29 22 29 30 29 43 27 29 25 32 29 44 36 63 29 22 25 25 32 43 25 35 25 42 29 30 25 41 29 29 41 33 29 22 25 22 35 30 25 29 50 41 63 41 22 29 25 53 42 29 30 29 25 27 73 78 76 25 35 30 25 69 50 58 0]xS 3558 5839 M (, which are coding)[22 25 54 42 23 27 42 25 41 30 29 25 27 35 41 23 43 0]xS 4144 5839 M (-)S LH (%%[Page: 6]%%) = %%PageTrailer %%Page: 7 7 %%PageBoundingBox: 12 12 599 779 %%EndPageComments %%BeginPageSetup /DeviceRGB dup setcolorspace /colspABC exch def mysetup concat colspRefresh %%EndPageSetup /DeviceGray dup setcolorspace /colspABC exch def 0 0 scol 650 578 M (direction )[41 23 30 29 27 25 23 35 43 0]xS 951 578 M (\(expressed transcript\) )[27 29 50 41 30 29 29 29 29 41 25 25 30 41 43 29 27 30 23 41 25 27 0]xS 1676 578 M (based assays, are aligned to the genome, the)[41 41 29 29 41 25 41 29 29 41 33 29 22 25 41 30 29 25 41 22 23 32 43 28 41 25 25 35 25 25 41 29 25 32 29 43 35 63 29 22 25 25 42 0]xS 3090 578 M (ir)[23 0]xS 3143 578 M ( orientation may be reversed with )[25 35 30 23 29 43 25 41 25 23 35 43 25 63 41 33 25 41 29 25 30 29 34 29 30 29 29 41 25 53 23 25 42 0]xS 650 691 M (respect to the genome. )[30 29 29 41 29 27 25 25 25 35 25 25 42 29 25 32 29 43 35 63 29 22 25 0]xS 1394 691 M ( )S F0S75 Ji 650 917 M (Run)[82 64 0]xS 861 917 M (ning the SNP Classifier)[65 32 65 63 29 36 65 55 29 59 99 72 29 79 29 56 49 49 33 35 33 55 0]xS 2017 917 M ( )S F1S64 Ji 650 1059 M (Once the coding information has been extracted from Ensembl, it is now possible to ) [78 51 42 42 25 29 51 42 25 42 51 50 23 51 45 25 23 51 32 51 33 77 41 28 23 51 51 25 51 41 36 25 51 42 42 51 25 42 46 29 33 41 42 29 42 50 25 32 33 50 77 25 66 51 36 42 77 51 23 22 25 23 29 25 23 36 25 51 51 67 25 51 51 37 36 23 51 23 42 25 29 51 0]xS 650 1172 M (determine how a polymorphism will affect any resultant proteins. Again, there are two ways ) [50 42 29 42 33 77 23 51 42 25 51 51 67 25 41 25 51 51 22 42 77 51 33 51 51 23 36 77 25 67 23 23 23 25 41 32 32 42 42 29 25 41 51 42 25 33 42 36 49 22 29 41 51 29 25 51 33 51 29 42 23 51 36 22 25 25 68 45 41 23 51 22 25 29 51 42 33 42 25 41 33 42 25 29 67 51 25 66 41 42 36 0]xS 650 1284 M (to classify SNPs. One is by a single template, the other)[29 51 25 42 23 41 36 36 23 32 42 25 48 77 56 36 22 25 25 78 51 42 25 23 36 26 51 42 25 41 25 36 23 51 45 23 42 25 29 42 77 51 23 41 28 42 22 25 29 51 42 25 50 29 51 42 0]xS 2786 1284 M ( is by batch.)[25 23 36 25 51 42 25 51 41 29 42 51 0]xS 3249 1284 M ( )S /F0S64 F0 [100 0 0 -100 0 0 ] mFS F0S64 Ji 650 1497 M (Classifying SNPs by Template)[68 26 48 42 42 28 30 47 28 55 54 25 51 84 61 42 25 55 47 25 69 47 84 55 26 48 31 0]xS 1940 1497 M ( )S F1S64 Ji 650 1634 M (The following script is the base case for classifying SNPs:)[61 51 42 25 32 51 23 23 51 67 23 51 45 25 36 42 33 23 51 29 25 23 36 25 29 51 42 25 51 41 36 42 25 42 41 36 42 25 32 51 33 25 42 23 41 36 36 23 32 42 23 51 45 25 47 77 56 36 0]xS 2869 1634 M ( )S 650 1747 M ( )S F6S53 Ji 650 1844 M (Classify_SNPs.pl)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1450 1844 M ( )S 650 1939 M ( )[50 50 50 50 50 50 50 0]xS 1050 1939 M (-)S 1100 1939 M (s )[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2250 1939 M ( )S 650 2033 M ( )[50 50 50 50 50 50 50 0]xS 1050 2033 M (-)S 1100 2033 M (c )[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2100 2033 M ( )S 650 2127 M ( )[50 50 50 50 50 50 50 0]xS 1050 2127 M (-)S 1100 2127 M (n )[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3050 2127 M ( )S 650 2222 M ( )[50 50 50 50 50 50 50 0]xS 1050 2222 M (-)S 1100 2222 M (o )[50 50 50 50 50 0]xS 2100 2222 M ( )S F1S64 Ji 650 2331 M ( )S 650 2444 M (The Query SNP File is the file described above as the alleles file. The coding info file and ) [61 51 42 25 77 49 42 33 42 25 48 77 56 25 56 23 23 42 25 23 36 25 29 51 42 25 32 23 23 42 25 50 42 36 42 33 23 51 42 50 25 41 51 51 46 42 25 41 36 25 29 51 42 25 41 23 23 42 22 42 36 25 32 23 23 42 22 25 25 61 51 42 25 42 51 50 23 51 44 25 23 51 32 51 25 32 23 23 42 25 41 51 50 0]xS 650 2556 M (the reference nucleotide sequence FASTA file are the files extracted from the extract coding ) [29 51 42 25 33 42 32 42 33 42 51 42 42 25 51 49 42 22 42 51 29 23 50 42 25 36 42 49 49 42 51 42 42 25 56 67 48 61 68 25 32 23 23 42 25 41 33 42 25 28 51 42 25 32 23 23 42 36 25 42 46 29 33 41 42 29 42 50 25 32 33 51 77 25 29 51 42 25 42 46 29 33 41 42 29 25 42 51 50 23 51 45 0]xS 650 2669 M (information section.)[23 51 32 51 33 77 41 29 23 51 51 25 36 42 42 29 23 51 51 0]xS 1433 2669 M ( The output file root is the prefix that)[25 25 61 51 42 25 51 49 29 51 49 29 25 32 23 23 42 25 33 51 51 29 25 23 36 25 29 51 42 25 51 33 42 33 23 46 25 29 51 41 0]xS 2913 2669 M ( will be applied to the output. )[25 67 23 23 23 25 51 42 24 41 51 51 23 23 42 50 25 29 51 25 28 51 42 25 51 49 29 51 49 29 22 25 0]xS 650 2781 M (Recall that two files will be generated, one normalized and one deno) [63 42 41 41 23 23 25 29 51 41 29 25 29 67 51 25 32 23 23 42 36 25 67 23 23 23 25 50 42 25 45 42 51 42 33 41 29 42 49 22 25 51 51 42 25 51 51 33 77 41 23 23 42 42 50 25 41 51 50 25 51 51 42 25 50 42 51 0]xS 3292 2781 M (r)S 3325 2781 M (malized. )[77 41 23 22 43 42 50 21 25 0]xS 3694 2781 M ( )S /F7S64 F7 [100 0 0 -100 0 0 ] mFS F7S64 Ji 650 2994 M (Mapping Amplicons to )[85 49 49 49 29 52 45 25 70 77 49 27 29 33 47 53 35 25 29 47 0]xS 1579 2994 M (Extracted Coding Information Coordinates)[65 56 29 35 49 33 29 40 50 25 66 47 50 29 52 45 25 37 52 28 47 35 77 49 30 29 47 52 25 66 47 47 35 50 29 52 49 29 40 0]xS 3291 2994 M ( )S F3S64 Ji 650 3131 M (Because the range of the extracted template used for primer design is often going) [56 29 27 41 43 29 29 25 25 42 29 25 30 41 43 32 29 25 35 22 25 25 42 29 25 29 50 25 30 41 27 25 29 41 25 25 29 63 41 22 41 25 29 24 43 29 29 41 25 22 35 30 25 41 30 23 63 29 30 25 41 28 29 23 32 43 25 23 29 25 35 22 25 29 43 25 32 35 23 43 0]xS 3236 3131 M ( to be different than the range )[25 25 35 25 41 29 25 41 23 22 22 29 30 29 44 25 25 25 42 41 43 25 25 42 29 25 30 40 43 32 29 0]xS 650 3244 M (extracted for coding information, unless the extracted template is in a gene sparse area, ) [29 50 25 30 41 27 25 29 41 25 22 35 30 25 27 35 41 23 43 32 25 23 43 22 35 30 63 41 25 23 35 43 22 25 43 43 22 29 29 29 25 25 42 29 25 29 50 25 30 41 27 25 29 41 25 25 29 62 41 22 41 24 29 25 23 29 25 23 43 25 41 25 32 29 43 29 25 29 41 41 30 29 29 25 41 30 29 41 22 0]xS 3505 3244 M (mapping from one to )[62 41 40 41 23 43 32 25 22 30 35 63 25 35 43 29 25 25 35 0]xS 650 3356 M (the other will be required even if the same version of the build and assembly are used. ) [25 42 29 25 35 25 42 29 30 25 53 23 22 22 25 41 29 25 30 29 43 43 23 30 29 41 25 29 34 29 43 25 23 22 25 25 42 29 25 29 41 63 29 25 34 29 30 29 23 35 43 25 35 22 25 25 42 29 25 41 43 23 22 41 24 41 43 41 25 41 29 29 29 62 41 22 33 25 41 30 29 25 43 29 29 41 22 25 0]xS 3473 3356 M ( )S 650 3469 M ( )S 650 3584 M (The output of this mapp)[58 42 29 25 35 43 25 41 43 25 25 35 22 25 25 42 23 29 25 63 40 41 0]xS 1452 3584 M (ing is )[23 43 32 25 23 29 0]xS 1651 3584 M (stored in the )[29 25 35 30 29 41 25 23 43 25 25 42 29 0]xS /F8S64 F8 [100 0 0 -100 0 0 ] mFS F8S64 Ji 2077 3584 M (run_offset)[60 60 60 60 60 60 60 60 60 0]xS F3S64 Ji 2677 3584 M ( file, which will be used when classifying SNPs )[25 22 23 22 29 22 25 53 42 23 27 42 25 53 23 22 22 25 41 29 24 43 29 29 41 25 53 42 29 42 25 27 22 41 29 29 23 22 33 23 43 32 25 50 78 53 29 0]xS 650 3697 M (by batch.)[41 33 25 41 41 25 27 42 0]xS 947 3697 M ( )S 650 3810 M ( )S F8S53 Ji 650 3908 M (Map_Amplicons_to_New_Template_by_batch.pl)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2700 3908 M ( )S 650 4003 M ( )[50 50 50 50 50 50 50 0]xS 1050 4003 M (-)S 1100 4003 M (a Primer Design Run directory \(where amplicon.fasta is\))[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 3850 4003 M ( )S 650 4097 M ( )[50 50 50 50 50 50 50 0]xS 1050 4097 M (-)S 1100 4097 M (l Target List)[50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1750 4097 M ( )S 650 4192 M ( )[50 50 50 50 50 50 50 0]xS 1050 4192 M (-)S 1100 4192 M (d New Template Directory)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2300 4192 M ( )S F3S64 Ji 650 4300 M ( )S 650 4413 M (T)S 708 4413 M (his script will read in the target list and compute the offsets for all of the amplicons in the primer design ) [42 23 29 25 29 27 30 23 41 25 25 53 23 22 22 25 30 29 41 41 25 23 43 25 25 42 29 25 25 41 29 32 29 25 25 22 23 29 25 25 41 43 41 25 27 35 63 41 43 25 29 25 25 42 29 25 35 22 22 29 29 25 29 24 22 35 30 25 41 22 22 25 35 22 25 25 42 29 25 41 63 41 22 23 27 35 43 29 25 23 43 25 24 42 29 24 41 30 23 63 29 30 25 41 29 29 23 32 43 0]xS 650 4525 M (directory. The output file will be placed in the directory specified by ) [41 23 30 29 27 25 35 30 33 22 25 25 25 58 42 29 25 35 43 25 41 43 25 25 22 23 22 29 25 53 23 22 22 25 41 29 25 41 22 41 27 29 41 25 22 43 25 25 42 29 25 41 23 30 29 27 25 35 30 33 25 29 41 29 27 23 22 23 29 41 25 41 33 0]xS 2895 4525 M (-)S 2921 4525 M (d under the target ID's directory with )[41 25 43 42 41 29 30 25 25 42 29 25 25 41 30 32 29 25 25 32 73 22 29 25 41 23 30 29 27 25 35 30 33 25 53 23 25 42 0]xS 650 4641 M (the filename )[25 42 29 25 22 23 22 29 43 40 63 29 0]xS F8S64 Ji 1067 4641 M (run_offset)[60 60 60 60 60 60 60 60 60 0]xS F3S64 Ji 1667 4641 M (. If a )[22 25 25 32 22 25 41 0]xS F8S64 Ji 1884 4641 M (r)S 1944 4641 M (un_offset )[60 60 60 60 60 60 60 60 60 0]xS F3S64 Ji 2544 4641 M (already exists, the old file will be copied over to )[41 22 30 29 41 41 33 25 29 50 23 29 25 29 22 25 25 42 29 25 35 22 41 25 22 23 22 29 25 53 23 22 22 25 41 29 25 26 35 41 23 29 41 25 35 34 29 30 25 25 35 0]xS F8S64 Ji 650 4757 M (run_offset.)[60 60 60 60 60 60 60 60 60 60 0]xS F3S64 Ji 1310 4757 M (, where is the date the previous file was last modified. The new file will ) [67 41 41 25 29 67 22 24 53 42 29 30 29 25 67 41 41 25 29 67 25 23 29 25 25 42 29 25 40 41 25 29 25 25 42 29 25 40 30 29 34 23 35 43 29 25 22 23 22 29 25 53 41 29 25 22 41 29 25 25 63 35 41 23 22 23 29 41 22 25 24 58 42 29 25 43 29 53 25 22 23 22 29 25 53 23 22 22 0]xS 650 4870 M (contain the old file, plus the new mapping offsets.)[27 35 43 25 41 23 43 25 25 42 29 25 35 22 41 25 22 23 22 29 22 25 40 22 43 29 25 25 42 29 25 43 28 53 25 63 41 41 40 23 43 32 25 35 22 22 29 29 25 29 0]xS 2249 4870 M ( )S F7S64 Ji 650 5082 M (Classifying SNP)[66 27 49 35 35 29 28 44 29 52 45 25 47 77 0]xS 1299 5082 M (s)S 1334 5082 M ( by Batch)[25 48 44 25 65 49 29 33 0]xS 1705 5082 M ( )S F3S64 Ji 650 5220 M (The script for c)[58 42 29 25 29 27 30 23 41 25 25 22 35 30 25 0]xS 1143 5220 M (lassifying SNP by batch is:)[22 41 29 29 23 22 33 23 43 32 25 50 78 53 26 41 33 25 41 41 25 27 42 25 23 29 0]xS 2046 5220 M ( )S 650 5332 M ( )S F8S53 Ji 650 5431 M (Classify_SNPs_by_Batch.pl)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1900 5431 M ( )S 650 5525 M ( [required])[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1550 5525 M ( )S 650 5620 M ( )[50 50 50 50 50 50 50 0]xS 1050 5620 M (-)S 1100 5620 M (l Target List)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2000 5620 M ( )S 650 5714 M ( )[50 50 50 50 50 50 50 0]xS 1050 5714 M (-)S 1100 5714 M (s Allele Freq Directory)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2500 5714 M ( )S 650 5809 M ( \(Needs to be writeable\))[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2600 5809 M ( )S LH (%%[Page: 7]%%) = %%PageTrailer %%Page: 8 8 %%PageBoundingBox: 12 12 599 779 %%EndPageComments %%BeginPageSetup /DeviceRGB dup setcolorspace /colspABC exch def mysetup concat colspRefresh %%EndPageSetup /DeviceGray dup setcolorspace /colspABC exch def 0 0 scol 650 564 M ( )[50 50 50 50 50 50 0]xS 1000 564 M ( )S 1050 564 M (-)S 1100 564 M (c Coding Info Directory )[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2550 564 M ( )S 650 658 M ( \(Where template.codin)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2500 658 M (g_info, template.fasta, and )[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 650 753 M (run_offset are\))[50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1400 753 M ( )S F3S64 Ji 650 861 M ( )S 650 974 M (When classifying SNPs by batch)[89 42 29 43 25 27 22 41 29 29 23 22 33 23 43 32 25 50 78 53 29 25 41 33 25 41 41 24 27 0]xS 1736 974 M ( you need to specify which targets to process. Typically this will be all the ) [25 33 35 43 25 43 29 29 41 25 25 35 25 29 41 29 27 23 22 33 25 53 42 23 27 42 25 25 41 30 32 29 25 29 25 25 35 25 41 30 35 28 29 29 29 22 25 25 58 33 41 23 27 41 22 22 33 25 25 42 23 29 25 53 23 22 22 25 41 29 25 41 22 22 25 25 42 29 0]xS 650 1086 M (files in the Allele Frequency directory. The files in the Allele Freq directory should have the name ) [22 23 22 29 29 25 23 43 25 25 42 29 25 76 22 22 29 22 29 25 57 30 29 43 43 29 43 27 33 25 41 22 30 29 27 25 35 30 33 22 25 26 58 42 29 25 22 23 22 29 29 25 23 43 25 25 42 29 25 76 22 22 29 22 29 25 57 30 29 43 25 41 23 30 29 27 25 35 30 33 26 29 42 35 43 22 41 25 42 41 34 29 25 25 42 29 24 43 41 63 29 0]xS 3894 1086 M (pattern of )[40 41 25 25 29 30 43 25 35 22 0]xS F8S64 Ji 650 1202 M (*_allele_frequencies.txt)[60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 0]xS F3S64 Ji 2090 1202 M (.)S 2112 1202 M ( )S 650 1315 M ( )S 650 1430 M (T)S 708 1430 M (he per line format of )[42 29 25 41 29 30 25 22 23 43 29 25 22 35 30 63 41 25 25 35 22 0]xS F8S64 Ji 1394 1430 M (*_allele_frequences.txt)[60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 0]xS F3S64 Ji 2774 1430 M ( is:)[25 23 29 0]xS 2873 1430 M ( )S 650 1544 M ()[67 41 29 32 23 43 0]xS 952 1544 M (\\)S 1002 1544 M (t)[25 67 29 42 41 0]xS 1273 1544 M (\\)S 1323 1544 M (t)[24 67 41 62 41 22 23 27 35 43 25 32 73 0]xS 1905 1544 M (\\)S 1955 1544 M (t)[25 67 41 22 22 29 22 29 46 0]xS 2325 1544 M (\\)S 2375 1544 M (t)[25 67 40 22 22 29 22 29 46 0]xS 2744 1544 M (\\)S 2794 1544 M (t)[25 67 22 30 29 43 43 29 43 27 33 0]xS 3252 1544 M (\\)S 3302 1544 M (n)S 3345 1544 M ( )S 650 1656 M ( )S 650 1772 M (T)S 708 1772 M (he input of the basis script )[42 29 25 23 43 41 43 25 25 35 22 25 25 42 29 25 41 41 29 23 29 25 29 27 30 23 41 25 0]xS F8S64 Ji 1595 1772 M (Classify_SNP.pl)[59 60 60 60 60 60 60 60 60 60 60 60 60 60 0]xS /F6S64 F6 [100 0 0 -100 0 0 ] mFS F6S64 Ji 2494 1772 M ( )S F3S64 Ji 2554 1772 M (is:)[23 29 0]xS 2628 1772 M ( )S 650 1885 M ()[67 41 29 32 23 43 0]xS 952 1885 M (\\)S 1002 1885 M (t)[25 67 29 42 41 0]xS 1273 1885 M (\\)S 1323 1885 M (t)[24 67 35 30 23 29 43 25 41 25 23 35 43 0]xS 1833 1885 M (\\)S 1883 1885 M (t)[25 67 41 22 22 29 22 29 25 22 23 29 25 0]xS 2331 1885 M (\\)S 2380 1885 M (n)S 2423 1885 M ( )S 650 1997 M ( )S 650 2110 M (S)S 700 2110 M (ince these two input files are different, the batch classification script will automatically convert the files before ) [23 43 27 29 25 25 42 29 29 29 25 25 53 35 25 23 43 41 43 25 25 22 23 22 29 29 25 41 30 29 25 41 23 22 22 29 30 29 43 25 22 25 25 42 29 25 40 41 25 27 42 25 27 22 41 29 29 23 22 23 27 41 24 23 35 43 25 29 27 30 23 41 25 25 53 23 22 22 25 41 43 25 35 62 41 25 23 27 41 22 22 33 25 27 35 43 34 29 30 25 25 25 42 29 25 22 23 22 29 29 25 41 29 22 35 30 29 0]xS 650 2225 M (sending them to the )[29 29 43 41 23 43 32 25 25 42 29 63 25 25 35 25 25 42 29 0]xS F8S64 Ji 1305 2225 M (Classify_SNP.pl)[60 60 60 60 60 59 60 60 60 60 60 60 60 60 0]xS F3S64 Ji 2204 2225 M ( )S 2229 2225 M (script. )[29 27 30 23 41 25 22 25 0]xS 2476 2225 M (\(This automatic conversion is performed with the help )[27 58 42 23 29 25 41 43 25 35 63 41 25 23 27 25 27 35 43 34 29 30 29 23 35 43 25 23 29 25 41 29 30 22 35 31 63 29 41 25 53 23 25 42 25 25 42 29 24 42 29 22 41 0]xS 650 2342 M (of )[35 22 0]xS F8S64 Ji 732 2342 M (Strip_Simple_SNPs_From_AlleleFrequen)[60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 0]xS 2892 2342 M (cy.pl)[60 60 60 60 0]xS F3S64 Ji 3192 2342 M (.\) )[22 27 0]xS 3266 2342 M (Also, if the range of the )[76 22 29 35 22 25 23 22 25 25 42 29 25 30 41 43 32 29 25 35 22 25 25 42 29 0]xS 650 2455 M (coding information extraction is different than the range of the template) [27 35 41 23 43 32 25 23 43 22 35 30 63 41 25 23 35 43 25 29 50 25 30 41 27 25 23 35 43 25 22 29 25 41 23 22 22 29 30 29 43 25 25 25 42 41 43 25 24 42 29 25 30 41 43 32 29 25 35 22 25 25 42 29 25 25 29 63 41 22 41 25 0]xS 2976 2455 M ( used for primer design)[25 43 29 29 41 24 22 35 30 25 41 30 23 63 29 30 25 41 29 29 23 32 0]xS 3717 2455 M (, )[22 0]xS 3764 2455 M (then )[25 42 29 43 0]xS 3928 2455 M (the )[25 42 29 0]xS 650 2570 M (proper coordinate translations will be performed in order to maintain compatibility. The ) [41 30 35 41 29 30 25 27 35 35 30 41 23 43 41 25 29 25 25 30 41 43 29 22 41 25 23 35 43 29 25 53 23 22 22 25 41 29 25 41 29 30 22 35 30 63 29 41 25 23 43 25 35 30 41 29 30 25 25 35 25 63 41 23 43 25 41 23 43 25 27 35 62 41 41 25 22 41 23 22 23 25 33 22 25 25 58 42 29 0]xS F8S64 Ji 3570 2570 M (run_offset)[59 60 60 60 60 60 60 60 60 0]xS F3S64 Ji 4169 2570 M ( )S 650 2683 M (file must be p)[22 23 22 29 25 63 43 29 25 25 41 29 25 0]xS 1092 2683 M (recomputed for this to work. )[30 29 27 35 63 40 43 25 29 41 25 22 35 30 25 25 41 23 29 25 25 35 25 53 35 30 52 22 0]xS 2036 2683 M ( )S F0S75 Ji 650 2910 M (QC\222ing SNP Classification)[93 79 29 33 65 63 29 59 99 72 29 79 30 56 48 49 33 35 32 55 56 37 33 60 0]xS 1968 2910 M ( )S F1S64 Ji 650 3052 M (The QC of SNP Classification is very important. Delivering false positive data to our ) [61 51 42 25 77 64 25 51 32 25 48 77 56 25 64 23 41 36 36 23 32 23 42 41 29 23 51 51 25 23 36 25 47 42 33 42 25 23 77 51 51 33 29 41 51 29 22 25 25 77 42 23 23 47 42 33 23 51 45 25 32 41 23 36 42 25 51 51 36 23 29 23 47 42 25 50 41 28 41 25 29 51 25 51 49 33 0]xS 650 3165 M (outside collaborators would be embarrassing, and not finding false negative data would ) [51 49 29 36 23 50 42 25 42 51 23 23 41 51 51 33 41 29 51 33 36 25 67 51 49 23 50 25 51 42 25 42 77 51 41 33 33 41 36 36 23 51 45 22 25 41 51 50 25 51 51 29 25 32 23 51 50 23 51 45 25 32 41 23 36 42 25 51 42 45 41 29 23 47 42 25 49 41 29 41 25 67 51 49 23 50 0]xS 650 3277 M (result in important findin)[33 42 36 49 23 29 25 23 51 25 23 77 51 51 33 29 41 51 29 25 32 23 51 50 23 0]xS 1626 3277 M (gs be)[46 36 25 51 0]xS 1826 3277 M (ing lost. As you ha)[23 51 45 25 23 51 36 29 22 25 25 68 36 25 42 51 49 25 51 0]xS 2569 3277 M (ve see)[47 42 24 36 42 0]xS 2802 3277 M (n)S 2853 3277 M ( from the algorithm )[25 32 33 51 77 25 29 51 42 25 41 23 45 51 33 23 29 51 77 0]xS 3641 3277 M (implemented)[23 77 51 23 42 77 42 51 29 42 0]xS 4148 3277 M ( )S 650 3390 M (above, there are many end nodes/leaves in the decision tree, some of which may only get ) [41 51 51 47 42 22 25 29 51 42 33 42 25 41 33 42 25 76 41 51 42 25 42 51 49 25 51 51 50 42 36 50 23 42 41 47 42 36 25 23 51 25 29 51 42 25 50 41 42 23 36 23 51 51 25 29 33 42 42 22 25 36 51 77 42 25 51 32 25 67 51 23 42 51 25 77 41 42 25 51 51 23 42 25 44 42 29 0]xS 650 3502 M (traversed a fraction of a percent of the time, which makes thorough testing difficult without ) [29 33 41 47 42 33 36 42 50 25 41 25 32 33 41 42 29 23 51 51 25 51 32 25 41 25 51 42 33 42 42 51 29 25 51 32 25 29 51 42 25 29 23 77 42 22 25 67 51 23 42 51 24 77 41 47 42 36 25 29 51 51 33 51 49 45 51 25 29 42 36 29 23 51 45 25 50 23 32 32 23 42 49 23 29 25 67 23 29 51 51 49 29 0]xS 650 3615 M (simulated )[36 23 77 49 23 41 29 42 50 0]xS 1045 3615 M (data, and simulated data, as you know )[50 41 29 41 22 25 41 51 50 25 36 23 77 49 23 40 29 42 50 25 50 41 29 41 22 25 41 36 25 42 51 49 25 47 51 50 67 0]xS 2531 3615 M (rarely)[33 41 33 41 23 0]xS 2744 3615 M ( represent)[25 33 42 51 33 42 36 42 51 0]xS 3128 3615 M (s)S 3164 3615 M ( reality.)[25 33 42 41 23 23 29 42 0]xS 3444 3615 M ( Because of this, it )[25 25 61 42 42 40 49 36 42 25 51 32 25 29 51 23 36 22 25 23 29 0]xS 650 3727 M (is important to periodically perform sanity checks of )[23 36 25 23 77 51 51 33 29 41 51 29 25 29 51 25 51 42 33 23 51 50 23 42 41 23 23 42 25 51 42 33 32 51 33 77 25 36 41 51 23 29 42 25 42 51 42 42 47 36 25 51 32 0]xS 2702 3727 M (expected and unexpected results, just in )[42 46 51 42 42 29 42 50 25 41 51 50 25 49 50 42 46 51 41 42 29 41 50 25 33 42 36 49 23 29 36 22 25 23 49 36 29 25 23 51 0]xS 650 3840 M (case there is a bug in the program, or )[42 41 36 42 25 29 51 42 33 42 25 23 36 25 41 25 51 49 45 25 23 51 25 29 51 42 24 51 33 51 45 33 41 77 22 25 51 33 0]xS 2110 3840 M (even if some parameters were in)[42 47 42 51 25 23 32 25 36 51 77 42 25 51 41 33 41 77 42 29 42 33 36 25 67 42 33 42 25 23 0]xS 3361 3840 M (corre)[42 51 33 33 0]xS 3562 3840 M (ctly specified that )[42 28 23 42 25 36 51 42 42 23 32 23 42 50 25 29 51 41 29 0]xS 650 3952 M (the programmer did not have the foresight to exception handle.) [29 51 42 25 51 33 51 45 33 41 77 77 42 33 25 50 23 50 25 51 51 29 25 51 41 47 42 25 29 51 42 25 32 51 33 42 36 23 45 51 29 25 29 51 25 42 46 42 42 50 29 23 51 51 25 51 41 51 50 23 42 0]xS 3115 3952 M ( )S F0S64 Ji 650 4165 M (Checking the Flanking Sequence)[68 55 47 47 53 28 55 54 25 31 55 47 25 61 26 48 55 54 28 55 54 26 51 47 55 55 47 55 47 0]xS 2051 4165 M ( )S F1S64 Ji 650 4302 M (One of the )[78 51 42 25 51 32 25 29 51 42 0]xS 1101 4302 M (easiest methods for a human to perform an end)[42 41 36 23 42 36 29 25 77 42 29 51 51 50 36 25 32 51 33 25 41 25 51 49 77 41 51 25 29 51 25 51 42 33 32 51 34 77 25 41 51 25 42 51 0]xS 2947 4302 M (-)S 2978 4302 M (to)[29 0]xS 3058 4302 M (-)S 3089 4302 M (end check of whether the )[42 51 50 25 42 51 42 42 47 25 51 31 25 67 51 42 29 51 42 33 25 29 51 42 0]xS 650 4415 M (classification algorithm does not have any position trans)[42 23 41 36 36 23 32 23 42 41 29 23 51 51 25 41 23 45 51 33 23 29 51 77 25 50 51 42 36 25 51 51 29 25 51 41 47 42 25 41 51 42 25 51 51 36 23 29 23 51 51 25 29 33 41 51 0]xS 2821 4415 M (lation errors is to check the flanking )[23 41 29 23 51 51 25 42 33 33 51 33 36 25 24 36 25 29 51 25 42 51 42 42 47 25 29 51 42 25 32 23 41 51 47 23 51 45 0]xS 650 4527 M (sequence that is reported in the output against the bases that were called in the trace file. ) [36 42 49 49 42 51 42 42 25 29 51 41 29 25 23 36 25 33 42 51 51 33 29 42 50 25 23 51 25 29 51 42 25 51 49 29 51 49 29 25 41 45 41 23 51 36 29 25 29 51 42 25 51 41 36 42 36 25 29 51 41 29 25 67 42 33 42 25 42 41 23 22 42 50 25 23 51 25 29 50 42 25 29 33 41 42 42 25 32 23 23 42 22 25 0]xS 4119 4527 M ( )S F0S64 Ji 650 4740 M (Verification )[67 47 34 28 30 28 47 48 31 28 52 55 0]xS 1170 4740 M (through)[31 56 34 52 55 54 0]xS 1507 4740 M ( a dbSNP Proxy)[25 48 26 56 55 51 84 61 26 61 34 52 50 0]xS 2183 4740 M ( )S F1S64 Ji 650 4877 M (An easy way to determine whether there are any problems with verifying amino acid ) [68 51 25 42 41 36 42 25 66 41 42 25 29 51 25 50 42 29 42 33 77 23 51 42 24 67 51 42 29 51 42 33 25 29 51 42 33 42 25 41 33 42 25 41 50 42 25 51 33 51 51 23 42 77 36 25 67 23 29 51 25 47 42 33 23 32 42 23 51 45 25 41 77 23 50 51 25 41 42 23 50 0]xS 650 4990 M (subs)[36 49 51 0]xS 822 4990 M (titutions is through SNPs that have been determined to exist in dbSNP already. Using ) [29 23 29 49 29 23 51 52 36 25 23 36 25 29 52 33 51 49 45 51 25 48 77 56 36 25 29 51 41 29 25 51 41 47 42 25 51 42 42 51 25 50 42 29 42 32 77 23 51 42 50 25 29 51 25 42 46 23 36 29 25 23 51 25 50 51 48 77 56 25 41 23 33 42 41 50 42 22 25 25 71 36 23 51 45 0]xS 650 5102 M (the rs ID, you can look up the SNP in Ensembl, and )[29 51 42 25 33 36 25 35 77 22 25 42 51 49 25 42 41 51 25 23 51 51 47 25 49 51 25 29 51 42 25 48 77 56 25 23 51 25 66 51 36 42 77 51 23 22 25 41 51 49 0]xS 2709 5102 M (then )[29 51 42 51 0]xS 2907 5102 M (ver)[47 42 0]xS 3029 5102 M (ify that the flanking sequences, )[23 32 42 25 29 51 41 29 25 29 51 42 25 32 23 41 51 47 22 51 45 25 36 42 49 49 42 51 42 42 36 22 0]xS 650 5215 M (the )[29 51 42 0]xS 797 5215 M (modified )[77 51 50 23 32 23 42 50 0]xS 1170 5215 M (codon and )[42 51 50 51 51 25 41 51 50 0]xS 1607 5215 M (the amino acid change are )[28 51 42 25 41 77 23 51 51 25 41 42 23 50 24 42 51 41 51 44 42 25 41 33 42 0]xS 2637 5215 M (the same. Also, if you are a)[29 51 42 25 36 41 77 42 22 25 25 68 23 36 51 22 25 23 32 25 42 51 49 25 41 33 41 25 0]xS 3705 5215 M (nalyzing )[51 41 23 42 42 23 51 45 0]xS 650 5327 M (many SNPs and a significant number )[77 41 51 42 25 48 77 56 36 25 41 51 50 25 41 25 36 23 45 51 23 32 23 41 41 51 29 25 51 49 77 51 42 33 0]xS 2109 5327 M (are)[41 33 0]xS 2225 5327 M ( )S 2250 5327 M (indicated to already )[23 51 50 23 42 41 29 42 50 25 28 51 25 41 23 33 42 41 50 42 0]xS 3027 5327 M (have )[51 40 47 42 0]xS 3232 5327 M (been )[51 41 42 51 0]xS 3442 5327 M (identified in dbSNP, )[23 50 42 51 29 22 32 23 42 50 25 23 51 25 50 51 48 77 56 22 0]xS 650 5440 M (then )[29 51 42 51 0]xS 848 5440 M (you should find that most of the SNPs should have the same allele type as dbSNP.) [42 51 49 25 36 51 51 49 23 50 25 32 23 51 50 25 29 51 41 29 25 77 51 36 29 25 51 32 25 29 51 42 25 48 77 57 36 25 36 51 51 49 23 50 26 51 41 47 42 25 29 51 42 25 36 41 77 42 25 40 23 23 42 23 42 25 28 42 51 42 25 40 36 25 50 51 48 77 56 0]xS 4043 5440 M ( It is )[25 25 35 29 25 24 36 0]xS 650 5552 M (uncommon for a single position substitution to be tri)[49 51 42 51 77 77 51 51 25 32 51 33 25 41 25 36 23 51 45 23 42 25 51 51 36 23 29 23 51 51 25 36 49 51 37 29 23 29 49 29 23 51 51 25 29 51 25 51 42 26 29 33 0]xS 2707 5552 M (-)S 2738 5552 M (allelic )[41 23 23 42 23 23 42 0]xS 2980 5552 M (p)S 3031 5552 M (osition.)[51 36 23 29 23 51 51 0]xS 3317 5552 M ( )S LH (%%[Page: 8]%%) = %%PageTrailer %%Page: 9 9 %%PageBoundingBox: 12 12 599 779 %%EndPageComments %%BeginPageSetup /DeviceRGB dup setcolorspace /colspABC exch def mysetup concat colspRefresh %%EndPageSetup /DeviceGray dup setcolorspace /colspABC exch def 0 0 scol F0S96 Ji 650 621 M (Allele Frequencies)[98 39 39 70 39 70 38 92 52 70 83 83 70 83 71 42 70 0]xS 1821 621 M ( )S F1S64 Ji 650 772 M (It is often important to estimate a variation\222s frequency within the sample population. For a ) [35 29 25 23 36 25 51 32 29 42 51 25 23 77 51 52 33 29 41 51 29 25 29 51 25 42 37 29 23 77 41 29 42 25 41 25 47 41 33 23 41 29 23 51 51 22 36 25 32 33 42 49 49 41 51 42 42 25 67 23 29 51 23 51 25 29 51 42 25 36 41 77 51 23 42 25 51 51 50 49 23 41 29 23 51 51 22 25 25 56 51 33 25 41 0]xS 650 884 M (given population sample selected by)[45 23 47 42 51 25 51 51 51 49 23 41 29 23 51 51 25 36 41 77 51 23 42 25 35 42 23 42 42 29 42 50 25 50 0]xS 2045 884 M ( a)[25 0]xS 2111 884 M ( phenotype of interest)[25 51 51 42 51 51 29 42 50 42 25 51 32 25 23 51 29 42 33 42 36 0]xS 2963 884 M (, if an allele variation exists that )[22 25 23 32 25 41 51 25 41 23 23 42 23 42 25 46 41 33 23 41 29 22 51 51 25 42 46 23 36 29 36 25 29 51 41 29 0]xS 650 997 M (has)[51 41 0]xS 778 997 M ( a higher degree of frequency than)[25 41 25 51 23 45 51 42 33 25 50 42 45 33 42 42 25 51 32 25 32 33 41 49 49 42 51 42 42 25 29 51 41 0]xS 2104 997 M ( that of)[25 29 51 41 29 25 51 0]xS 2387 997 M ( the reference/wild type allele, which is )[25 29 51 42 25 33 41 32 42 33 42 51 42 42 50 67 23 23 50 25 29 42 50 42 25 41 23 22 42 23 42 22 24 66 51 23 42 51 25 23 36 0]xS 650 1109 M (assume)[41 36 36 49 77 0]xS 931 1109 M (d)S 981 1109 M ( )S 1006 1109 M (t)S 1035 1109 M (o not be exhibiting the selected phenotype, then this correlation between ) [51 25 51 51 29 25 51 42 25 42 46 51 23 51 23 29 23 51 45 25 29 51 42 25 36 42 23 42 42 29 42 50 25 51 51 42 51 51 28 42 51 41 22 25 29 51 42 51 25 29 51 23 36 25 42 51 33 33 42 23 41 29 23 51 51 25 51 42 29 67 42 42 51 0]xS 3882 1109 M (this )[29 51 23 36 0]xS 650 1222 M (variant )[47 41 33 23 41 51 29 0]xS 940 1222 M (allele and )[41 23 23 42 22 42 25 41 51 50 0]xS 1325 1222 M (selected )[36 42 23 41 42 29 42 50 0]xS 1654 1222 M (phenotype might )[51 51 42 51 51 29 42 51 42 25 77 23 45 51 29 0]xS 2339 1222 M (exist)[42 46 23 36 0]xS 2515 1222 M (.)S 2537 1222 M ( )S 650 1334 M ( )S 650 1447 M (A variant is identified when a polymorphism exists between at leas) [68 25 47 41 33 23 41 51 29 25 23 36 25 23 50 42 51 29 23 32 23 42 50 25 67 51 41 51 25 41 25 51 51 23 42 77 51 33 51 51 23 36 77 25 42 46 23 36 29 36 25 52 42 29 67 42 42 51 24 41 29 25 23 42 41 0]xS 3222 1447 M (t one of the donor\222s )[29 25 51 51 42 25 51 32 25 29 51 42 24 50 51 51 51 33 22 36 0]xS 650 1559 M (haplotype)[51 41 51 23 51 29 42 51 0]xS 1031 1559 M (s and the reference. For a given position, the )[36 25 41 51 50 25 29 51 42 25 33 42 32 42 33 41 51 42 42 22 25 25 56 51 33 25 41 25 45 23 47 42 51 25 51 51 36 23 29 23 51 51 21 25 29 51 42 0]xS 2808 1559 M (allele)[41 23 23 42 22 0]xS 3001 1559 M ( of the individual could be )[25 51 32 25 29 51 42 25 23 51 50 23 47 23 50 49 40 23 25 42 51 49 23 50 25 51 42 0]xS 650 1672 M (heterozygous or homozygous, both of which would be obvious with respect to the reference ) [51 42 29 42 33 51 43 42 45 51 49 36 25 51 33 25 51 51 77 51 43 42 44 51 49 36 22 25 51 51 29 51 25 51 32 25 67 51 23 42 51 25 67 51 49 23 50 25 51 42 25 51 51 47 23 51 49 36 25 67 23 29 51 25 33 42 36 51 42 42 29 25 29 51 25 29 51 42 25 33 42 32 42 33 42 51 42 42 0]xS 650 1784 M (allele)[41 23 23 42 23 0]xS 844 1784 M (. When we compute allele frequencies, we are int)[22 25 24 89 51 42 51 24 67 42 25 42 51 77 51 49 29 42 24 41 23 23 42 23 42 25 32 33 42 49 49 42 50 42 23 42 36 22 25 66 42 25 41 33 42 25 22 51 0]xS 2753 1784 M (erested in determining what )[42 33 42 36 29 42 50 25 23 51 25 50 42 29 42 33 77 23 51 23 51 45 25 67 51 41 29 0]xS 650 1897 M (percentage of the alleles we have sampled is the)[51 42 33 42 42 51 29 41 45 42 25 51 32 25 29 51 42 24 41 23 23 42 22 42 36 25 67 42 25 51 41 47 42 25 36 41 77 51 23 42 50 25 23 36 25 29 51 0]xS 2492 1897 M ( variant)[25 46 41 33 23 41 51 0]xS 2781 1897 M (. )[22 25 0]xS 2853 1897 M ( )S 650 2009 M ( )S 650 2122 M (Assuming)[68 36 36 49 77 23 51 0]xS 1035 2122 M <20915292>[25 22 63 0]xS 1167 2122 M ( is the allele of the reference, )[25 23 36 25 29 51 42 25 41 23 23 42 23 42 24 51 32 25 29 51 42 25 33 42 32 42 33 42 51 42 42 22 0]xS 2302 2122 M (\221V\222 is the allele of the variant)[22 68 22 25 23 36 25 29 51 41 25 41 23 23 42 23 42 25 51 32 25 29 51 42 25 46 41 33 23 41 51 0]xS 3407 2122 M (, and \221)[22 25 41 51 50 25 0]xS 3642 2122 M (N)S 3719 2122 M <92>S 3741 2122 M ( is unknown)[25 23 36 25 49 51 47 51 51 67 0]xS 4217 2122 M (, )[22 0]xS 650 2234 M (we can use the chromosomes associated with the variant and total chr) [67 42 25 42 41 51 25 49 36 42 25 29 51 42 24 42 51 33 51 77 51 36 51 77 42 36 25 41 36 36 51 42 23 41 29 42 50 25 67 23 29 51 25 29 51 42 25 46 41 33 23 41 51 29 25 41 51 50 25 29 51 29 41 23 25 42 51 0]xS 3351 2234 M (omosomes successfully )[51 77 51 36 51 77 42 36 25 36 49 42 42 42 36 36 32 49 23 23 42 0]xS 650 2347 M (assayed to estimate the variant\222s frequency)[41 36 36 41 42 42 50 25 29 51 25 42 36 29 23 77 41 29 42 25 29 51 42 25 47 40 33 23 41 51 29 22 36 25 32 33 42 49 49 42 51 42 0]xS 2288 2347 M (.)S 2310 2347 M ( )S 650 2459 M ( )S F0S64 Ji 699 2576 M (Allele 1)[66 26 26 47 26 47 25 0]xS 1002 2576 M ( )S 1146 2576 M (Allele 2)[66 26 26 47 26 47 25 0]xS 1456 2576 M ( )S 1754 2576 M (Type)[69 47 55 0]xS 1972 2576 M ( )S 2310 2576 M (Chr\222s)[68 55 34 25 0]xS 2534 2576 M ( Assoc)[25 66 42 42 52 0]xS 2808 2576 M (\222d w/)[25 55 25 71 0]xS 3039 2576 M ( Variant)[25 67 48 34 28 47 55 0]xS 3374 2576 M ( )S 3573 2576 M (Chr\222s Counted)[68 55 34 25 42 25 68 52 55 55 31 47 0]xS 4185 2576 M ( )S : N 624 2486 4 4 rp C L ; : N 624 2486 4 4 rp C L ; : N 628 2486 446 4 rp C L ; : N 1074 2486 4 4 rp C L ; : N 1078 2486 446 4 rp C L ; : N 1524 2486 4 4 rp C L ; : N 1528 2486 671 4 rp C L ; : N 2199 2486 4 4 rp C L ; : N 2203 2486 1279 4 rp C L ; : N 3482 2486 4 4 rp C L ; : N 3486 2486 786 4 rp C L ; : N 4272 2486 4 4 rp C L ; : N 4272 2486 4 4 rp C L ; : N 624 2490 4 112 rp C L ; : N 1074 2490 4 112 rp C L ; : N 1524 2490 4 112 rp C L ; : N 2199 2490 4 112 rp C L ; : N 3482 2490 4 112 rp C L ; : N 4272 2490 4 112 rp C L ; F1S64 Ji 819 2692 M (R)S 882 2692 M ( )S 1269 2692 M (R)S 1332 2692 M ( )S 1603 2692 M (Homozygous)[76 51 77 51 43 42 45 51 49 0]xS 2124 2692 M ( )S 2819 2692 M (0)S 2866 2692 M ( )S 3855 2692 M (2)S 3902 2692 M ( )S : N 624 2602 4 4 rp C L ; : N 628 2602 446 4 rp C L ; : N 1074 2602 4 4 rp C L ; : N 1078 2602 446 4 rp C L ; : N 1524 2602 4 4 rp C L ; : N 1528 2602 671 4 rp C L ; : N 2199 2602 4 4 rp C L ; : N 2203 2602 1279 4 rp C L ; : N 3482 2602 4 4 rp C L ; : N 3486 2602 786 4 rp C L ; : N 4272 2602 4 4 rp C L ; : N 624 2606 4 113 rp C L ; : N 1074 2606 4 113 rp C L ; : N 1524 2606 4 113 rp C L ; : N 2199 2606 4 113 rp C L ; : N 3482 2606 4 113 rp C L ; : N 4272 2606 4 113 rp C L ; 817 2809 M (V)S 885 2809 M ( )S 1269 2809 M (R)S 1332 2809 M ( )S 1594 2809 M (Heterozygous)[76 42 29 42 33 51 43 42 45 51 49 0]xS : 2133 2723 66 112 rc 2133 2809 M ( )S ; 2819 2809 M (1)S 2866 2809 M ( )S 3855 2809 M (2)S 3902 2809 M ( )S : N 624 2719 4 4 rp C L ; : N 628 2719 446 4 rp C L ; : N 1074 2719 4 4 rp C L ; : N 1078 2719 446 4 rp C L ; : N 1524 2719 4 4 rp C L ; : N 1528 2719 671 4 rp C L ; : N 2199 2719 4 4 rp C L ; : N 2203 2719 1279 4 rp C L ; : N 3482 2719 4 4 rp C L ; : N 3486 2719 786 4 rp C L ; : N 4272 2719 4 4 rp C L ; : N 624 2723 4 113 rp C L ; : N 1074 2723 4 113 rp C L ; : N 1524 2723 4 113 rp C L ; : N 2199 2723 4 113 rp C L ; : N 3482 2723 4 113 rp C L ; : N 4272 2723 4 113 rp C L ; 819 2926 M (R)S 882 2926 M ( )S 1267 2926 M (V)S 1335 2926 M ( )S 1594 2926 M (Heterozygous)[76 42 29 42 33 51 43 42 45 51 49 0]xS : 2133 2840 66 112 rc 2133 2926 M ( )S ; 2819 2926 M (1)S 2866 2926 M ( )S 3855 2926 M (2)S 3902 2926 M ( )S : N 624 2836 4 4 rp C L ; : N 628 2836 446 4 rp C L ; : N 1074 2836 4 4 rp C L ; : N 1078 2836 446 4 rp C L ; : N 1524 2836 4 4 rp C L ; : N 1528 2836 671 4 rp C L ; : N 2199 2836 4 4 rp C L ; : N 2203 2836 1279 4 rp C L ; : N 3482 2836 4 4 rp C L ; : N 3486 2836 786 4 rp C L ; : N 4272 2836 4 4 rp C L ; : N 624 2840 4 112 rp C L ; : N 1074 2840 4 112 rp C L ; : N 1524 2840 4 112 rp C L ; : N 2199 2840 4 112 rp C L ; : N 3482 2840 4 112 rp C L ; : N 4272 2840 4 112 rp C L ; 817 3042 M (V)S 885 3042 M ( )S 1267 3042 M (V)S 1335 3042 M ( )S 1603 3042 M (Homozygous)[76 51 77 51 43 42 45 51 49 0]xS 2124 3042 M ( )S 2819 3042 M (2)S 2866 3042 M ( )S 3855 3042 M (2)S 3902 3042 M ( )S : N 624 2952 4 4 rp C L ; : N 628 2952 446 4 rp C L ; : N 1074 2952 4 4 rp C L ; : N 1078 2952 446 4 rp C L ; : N 1524 2952 4 4 rp C L ; : N 1528 2952 671 4 rp C L ; : N 2199 2952 4 4 rp C L ; : N 2203 2952 1279 4 rp C L ; : N 3482 2952 4 4 rp C L ; : N 3486 2952 786 4 rp C L ; : N 4272 2952 4 4 rp C L ; : N 624 2956 4 113 rp C L ; : N 1074 2956 4 113 rp C L ; : N 1524 2956 4 113 rp C L ; : N 2199 2956 4 113 rp C L ; : N 3482 2956 4 113 rp C L ; : N 4272 2956 4 113 rp C L ; 812 3159 M (N)S 889 3159 M ( )S 1262 3159 M (N)S 1339 3159 M ( )S 1669 3159 M (Unknown)[71 51 47 51 51 67 0]xS 2058 3159 M ( )S 2819 3159 M (0)S 2866 3159 M ( )S 3855 3159 M (0)S 3902 3159 M ( )S : N 624 3069 4 4 rp C L ; : N 628 3069 446 4 rp C L ; : N 1074 3069 4 4 rp C L ; : N 1078 3069 446 4 rp C L ; : N 1524 3069 4 4 rp C L ; : N 1528 3069 671 4 rp C L ; : N 2199 3069 4 4 rp C L ; : N 2203 3069 1279 4 rp C L ; : N 3482 3069 4 4 rp C L ; : N 3486 3069 786 4 rp C L ; : N 4272 3069 4 4 rp C L ; : N 624 3073 4 113 rp C L ; : N 624 3186 4 4 rp C L ; : N 624 3186 4 4 rp C L ; : N 628 3186 446 4 rp C L ; : N 1074 3073 4 113 rp C L ; : N 1074 3186 4 4 rp C L ; : N 1078 3186 446 4 rp C L ; : N 1524 3073 4 113 rp C L ; : N 1524 3186 4 4 rp C L ; : N 1528 3186 671 4 rp C L ; : N 2199 3073 4 113 rp C L ; : N 2199 3186 4 4 rp C L ; : N 2203 3186 1279 4 rp C L ; : N 3482 3073 4 113 rp C L ; : N 3482 3186 4 4 rp C L ; : N 3486 3186 786 4 rp C L ; : N 4272 3073 4 113 rp C L ; : N 4272 3186 4 4 rp C L ; : N 4272 3186 4 4 rp C L ; 650 3276 M ( )S 650 3388 M (Because some assays for)[61 42 42 41 49 36 42 25 36 51 77 42 25 41 36 36 41 42 36 25 32 51 0]xS 1592 3388 M ( a particular region may fail, the number of chromosomes counted ) [25 41 25 51 41 33 29 23 42 49 23 41 33 25 33 42 45 23 51 51 25 77 41 42 25 32 41 22 23 21 25 29 51 42 25 51 49 77 51 42 33 25 51 32 25 42 51 33 51 77 51 36 52 77 42 36 25 42 51 49 51 29 42 50 0]xS 650 3501 M (may not equal to the number of donors. Also, since multiple amplicons may assay the same ) [77 41 42 25 51 51 29 25 42 49 49 41 23 25 29 51 25 29 51 42 25 51 49 76 51 42 33 25 51 32 25 50 51 51 51 33 36 22 25 25 68 23 36 51 22 26 36 23 51 42 42 25 77 49 23 29 23 51 23 42 25 41 77 51 23 23 42 51 51 36 25 77 41 42 24 40 36 36 41 42 25 29 51 42 25 36 41 77 42 0]xS 650 3613 M (region because of amplicon tiling overlap, a given position with respect to the reference ) [33 42 45 23 51 51 25 51 42 42 41 49 36 42 25 51 32 25 41 77 51 23 22 42 50 51 25 29 23 23 23 51 45 25 51 47 42 33 23 41 51 22 25 41 24 45 23 47 42 51 25 50 51 36 23 29 23 51 51 25 67 23 29 51 25 33 42 36 51 42 42 29 25 29 51 25 29 51 42 25 33 42 32 42 33 42 51 42 42 0]xS 650 3726 M (coordinate )[42 51 51 33 50 23 51 41 29 42 0]xS 1088 3726 M (may have different ra)[77 41 42 25 50 41 47 42 25 50 23 32 32 41 33 42 51 29 25 33 0]xS 1910 3726 M (tes of success, and as a result)[29 42 36 25 51 32 25 36 49 42 42 42 36 36 22 25 41 51 50 26 41 36 25 41 25 33 42 36 49 23 0]xS 3028 3726 M ( have )[25 51 41 47 42 0]xS 3259 3726 M (different computed )[50 23 32 32 42 33 42 51 29 25 41 51 77 51 49 29 42 50 0]xS 650 3838 M (variant frequencies. )[47 41 33 23 41 51 29 25 32 33 42 49 49 42 51 42 23 42 36 22 25 0]xS 1453 3838 M ( For a successful assay size that contains enough data points to be ) [25 56 51 33 25 41 25 36 49 42 42 42 36 36 32 49 23 25 41 36 36 41 42 25 36 23 43 42 25 29 51 41 29 25 42 51 51 29 41 23 51 36 25 42 51 51 49 45 51 25 50 41 29 41 25 51 51 22 51 29 36 25 29 51 25 51 42 0]xS 650 3951 M (representative of )[33 42 51 33 42 36 42 51 29 41 29 23 47 42 25 51 32 0]xS 1324 3951 M (actual )[41 42 29 49 41 23 0]xS 1573 3951 M (allele frequencies, the computed allele frequencies for a given ) [41 23 22 42 23 42 25 32 33 42 49 49 42 51 42 22 42 36 22 25 29 51 42 25 42 51 77 50 49 29 42 50 25 41 23 23 42 22 42 25 32 33 42 49 49 42 51 42 23 42 36 25 32 51 33 25 41 25 45 23 47 42 51 0]xS 650 4063 M (position should be very close)[51 51 36 23 29 23 51 51 25 36 51 51 49 23 50 25 51 42 25 47 42 33 42 25 42 23 51 36 0]xS 1776 4063 M ( to other values )[25 29 51 25 51 29 51 42 33 25 47 41 23 49 42 36 0]xS 2400 4063 M (generated )[45 42 51 42 33 40 29 42 50 0]xS 2799 4063 M (from overlapping amplicons)[32 33 51 77 25 51 47 42 33 23 41 51 51 23 51 45 25 41 77 51 23 23 42 51 51 0]xS 3895 4063 M (.)S 3917 4063 M ( )S 650 4176 M ( )S 650 4288 M (The variant allele frequency for a given position is the number of chromosomes associated ) [61 51 42 25 47 41 33 23 41 51 29 25 41 23 23 42 22 42 25 32 33 42 49 49 42 50 42 42 25 32 51 33 25 41 25 45 23 47 42 51 25 51 51 36 23 29 23 51 51 25 23 36 25 29 51 42 25 51 49 77 51 42 33 25 51 32 25 42 51 33 51 77 51 36 52 77 42 36 25 41 36 36 51 42 23 41 29 42 50 0]xS 650 4401 M (with the variant divided by the number of chromosomes counted.) [67 23 29 51 25 29 51 42 25 47 41 33 23 41 51 29 25 50 23 47 23 49 42 50 25 51 42 25 29 51 42 25 51 49 77 51 42 33 25 51 32 25 42 51 33 51 77 51 37 51 77 42 36 25 42 51 49 51 29 42 50 0]xS 3201 4401 M ( )S F0S75 Ji 650 4627 M (Computing Frequenc)[79 61 99 64 65 36 33 65 63 29 72 40 54 65 64 55 64 0]xS 1713 4627 M (ies of Variations)[33 55 49 29 61 35 29 78 56 40 33 55 37 33 60 65 0]xS 2510 4627 M ( )S F1S64 Ji 650 4770 M (The frequency of variations can be computed with the following program:) [61 51 42 25 32 33 42 49 49 42 51 42 42 25 51 32 25 47 41 33 23 41 29 23 50 51 36 25 42 41 51 25 51 42 25 42 51 77 51 49 29 42 50 25 67 23 29 51 24 29 51 42 25 32 51 23 23 51 67 23 51 45 25 51 33 51 45 33 41 77 0]xS 3521 4770 M ( )S 650 4882 M ( )S F6S53 Ji 650 4980 M (Compute_SNP_Frequencies.pl)[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 1950 4980 M ( )S 650 5074 M ( )[50 50 50 50 50 50 50 0]xS 1050 5074 M (-)S 1100 5074 M (s )[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 0]xS 2200 5074 M ( )S 650 5168 M ( )[50 50 50 50 50 50 50 0]xS 1050 5168 M (-)S 1100 5168 M (f