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@HD VN:1.17 SO:unknown
@SQ SN:T1 LN:40
@SQ SN:T2 LN:40
@CO @SQ SN* LN* AH AN AS DS M5 SP TP UR
@CO @RG ID* BC CN DS DT FO KS LB PG PI PL PM PU SM
@CO @PG ID* PN CL PP DS VN
@CO this is a dummy alignment file to demonstrate different abilities of hts apis
@CO QNAME FLAG RNAME POS MAPQ CIGAR RNEXT PNEXT TLEN SEQ QUAL [TAG:TYPE:VALUE]…
@CO 1234567890123456789012345678901234567890
@CO AAAAACTGAAAACCCCTTTTGGGGACTGTTAACAGTTTTT T1
@CO TTTTCCCCACTGAAAACCCCTTTTGGGGACTGTTAACAGT T2
@CO ITR1-ITR2M, ITR2-ITR2M are proper pairs in T1 and T2, UNMP1 is partly mapped and pair is unmapped, UNMP2 & 3 are unmapped
@CO A1-A2, A4-A3 are proper pairs with A4-A3 in different read order. A5 is secondary alignment
ITR1 99 T1 5 40 4M = 33 10 ACTG ()()
ITR2 147 T2 23 49 2M = 35 -10 TT **
ITR2M 99 T2 35 51 2M = 23 10 AA &&
ITR1M 147 T1 33 37 4M = 5 -10 ACTG $$$$
UNMP1 73 T1 21 40 3M * 0 5 GGG &&1
UNMP2 141 * 0 0 * * 0 7 AA &&
UNMP3 77 * 0 0 * * 0 5 GGG &&2
A1 99 T1 25 35 6M = 31 8 ACTGTT ******
A2 147 T1 31 33 6M = 25 -8 ACTGTT ()()()
A3 147 T2 23 47 2M1X = 12 -5 TTG (((
A4 99 T2 12 50 3M = 23 5 GAA ()(
A5 355 T1 25 35 4M = 33 5 ACTG PPPP
B1 99 T1 25 35 6M = 31 8 GCTATT ******
B3 147 T2 23 47 2M1X = 12 -5 TAG (((
B4 99 T2 12 50 3M = 23 5 GAT ()(
B5 355 T1 25 35 4M = 33 5 AGTG PPPP
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