File: testEqWithOrig.sam

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@SQ	SN:1	LN:247249719
@SQ	SN:2	LN:242951149
@SQ	SN:3	LN:199501827
@SQ	SN:4	LN:191273063
@SQ	SN:5	LN:180857866
@SQ	SN:6	LN:170899992
@SQ	SN:7	LN:158821424
@SQ	SN:8	LN:146274826
@SQ	SN:9	LN:140273252
@SQ	SN:10	LN:135374737
@SQ	SN:11	LN:134452384
@SQ	SN:12	LN:132349534
@SQ	SN:13	LN:114142980
@SQ	SN:14	LN:106368585
@SQ	SN:15	LN:100338915
@SQ	SN:16	LN:88827254
@SQ	SN:17	LN:78774742
@SQ	SN:18	LN:76117153
@SQ	SN:19	LN:63811651
@SQ	SN:20	LN:62435964
@SQ	SN:21	LN:46944323
@SQ	SN:22	LN:49691432
@SQ	SN:X	LN:154913754
01:====	73	1	10011	0	4M	=	10009	0	CCTA	I00?
02:===X	73	1	10011	0	4M	=	10009	0	CCTT	I00?
03:==X=	73	1	10011	0	4M	=	10009	0	CCAA	I00?
04:==XX	73	1	10011	0	4M	=	10009	0	CCAT	I00?
05:=X==	73	1	10011	0	4M	=	10009	0	CTTA	I00?
06:=X=X	73	1	10011	0	4M	=	10009	0	CTTT	I00?
07:=XX=	73	1	10011	0	4M	=	10009	0	CTAA	I00?
08:=XXX	73	1	10011	0	4M	=	10009	0	CTAT	I00?
09:X===	73	1	10011	0	4M	=	10009	0	TCTA	I00?
10:X==X	73	1	10011	0	4M	=	10009	0	TCTT	I00?
11:X=X=	73	1	10011	0	4M	=	10009	0	TCAA	I00?
12:X=XX	73	1	10011	0	4M	=	10009	0	TCAT	I00?
13:XX==	73	1	10011	0	4M	=	10009	0	TTTA	I00?
14:XX=X	73	1	10011	0	4M	=	10009	0	TTTT	I00?
15:XXX=	73	1	10011	0	4M	=	10009	0	TTAA	I00?
16:XXXX	73	1	10011	0	4M	=	10009	0	TTAT	I00?
01:====	73	1	10011	0	4M	=	10009	0	====	I00?
02:===X	73	1	10011	0	4M	=	10009	0	===T	I00?
03:==X=	73	1	10011	0	4M	=	10009	0	==A=	I00?
04:==XX	73	1	10011	0	4M	=	10009	0	==AT	I00?
05:=X==	73	1	10011	0	4M	=	10009	0	=T==	I00?
06:=X=X	73	1	10011	0	4M	=	10009	0	=T=T	I00?
07:=XX=	73	1	10011	0	4M	=	10009	0	=TA=	I00?
08:=XXX	73	1	10011	0	4M	=	10009	0	=TAT	I00?
09:X===	73	1	10011	0	4M	=	10009	0	T===	I00?
10:X==X	73	1	10011	0	4M	=	10009	0	T==T	I00?
11:X=X=	73	1	10011	0	4M	=	10009	0	T=A=	I00?
12:X=XX	73	1	10011	0	4M	=	10009	0	T=AT	I00?
13:XX==	73	1	10011	0	4M	=	10009	0	TT==	I00?
14:XX=X	73	1	10011	0	4M	=	10009	0	TT=T	I00?
15:XXX=	73	1	10011	0	4M	=	10009	0	TTA=	I00?
16:XXXX	73	1	10011	0	4M	=	10009	0	TTAT	I00?
01:====	73	1	10011	0	4M	=	10009	0	C===	I00?
02:===X	73	1	10011	0	4M	=	10009	0	=C=T	I00?
03:==X=	73	1	10011	0	4M	=	10009	0	==AA	I00?
04:==XX	73	1	10011	0	4M	=	10009	0	==AT	I00?
05:=X==	73	1	10011	0	4M	=	10009	0	=TTA	I00?
06:=X=X	73	1	10011	0	4M	=	10009	0	CT=T	I00?
07:=XX=	73	1	10011	0	4M	=	10009	0	=TAA	I00?
08:=XXX	73	1	10011	0	4M	=	10009	0	=TAT	I00?
09:X===	73	1	10011	0	4M	=	10009	0	T=TA	I00?
10:X==X	73	1	10011	0	4M	=	10009	0	TC=T	I00?
11:X=X=	73	1	10011	0	4M	=	10009	0	TCA=	I00?
12:X=XX	73	1	10011	0	4M	=	10009	0	TCAT	I00?
13:XX==	73	1	10011	0	4M	=	10009	0	TT=A	I00?
14:XX=X	73	1	10011	0	4M	=	10009	0	TT=T	I00?
15:XXX=	73	1	10011	0	4M	=	10009	0	TTA=	I00?
16:XXXX	73	1	10011	0	4M	=	10009	0	TTAT	I00?
Read:GGCCTA;Ref:CCTA	73	1	10011	0	2S4M	=	10009	0	GGC=T=	??I00?
Read:CCTA;Ref:CCTA	73	1	10011	0	4M4H	=	10009	0	C=T=	I00?
Read:CCGTxxxC;Ref:CCxTAACC	73	1	10011	0	1M1P1M1I1M3D1M	=	10009	0	C=GT=	I00??
Read:CCxxAC;Ref:CCTAACC	73	1	10011	0	2M2N2M	=	10009	0	C=A=	I00?
chromNotInRef	73	2	10011	0	4M	=	10009	0	CCTA	I00?
chromNotInRef1	73	2	10011	0	4M	=	10009	0	CC=A	I00?