@SQ SN:zz LN:30 @CO All MD and NM should match the stored values a1 0 zz 6 1 10M * 0 0 AAAAATTTTT * co:Z:no fields a2 0 zz 6 1 10M * 0 0 AAAAGGTTTT * a3 0 zz 6 1 10M * 0 0 GAAAATTTTG * i1 0 zz 6 1 5M1I5M * 0 0 AAAAAGTTTTT * i2 0 zz 6 1 5M3I5M * 0 0 AAAAAGGGTTTTT * i3 0 zz 6 1 10M2I * 0 0 AAAAATTTTTCC * i4 0 zz 6 1 10M2P2I * 0 0 AAAAATTTTTCC * d1 0 zz 6 1 5M10D5M * 0 0 AAAAACCCCC * d2 0 zz 6 1 5M10N5M * 0 0 AAAAACCCCC * sid 0 zz 6 1 1S4M10D5I4M1S * 0 0 AAAAAGGGGGCCCCC * A1 0 zz 6 1 10M * 0 0 AAAAATTTTT * MD:Z:10 NM:i:0 co:Z:correct fields A2 0 zz 6 1 10M * 0 0 AAAAGGTTTT * MD:Z:4A0T4 NM:i:2 A3 0 zz 6 1 10M * 0 0 GAAAATTTTG * MD:Z:0A8T0 NM:i:2 I1 0 zz 6 1 5M1I5M * 0 0 AAAAAGTTTTT * MD:Z:10 NM:i:1 I2 0 zz 6 1 5M3I5M * 0 0 AAAAAGGGTTTTT * MD:Z:10 NM:i:3 I3 0 zz 6 1 10M2I * 0 0 AAAAATTTTTCC * MD:Z:10 NM:i:2 I4 0 zz 6 1 10M2P2I * 0 0 AAAAATTTTTCC * MD:Z:10 NM:i:2 D1 0 zz 6 1 5M10D5M * 0 0 AAAAACCCCC * MD:Z:5^TTTTTTTTTT5 NM:i:10 D2 0 zz 6 1 5M10N5M * 0 0 AAAAACCCCC * MD:Z:10 NM:i:0 SID 0 zz 6 1 1S4M10D5I4M1S * 0 0 AAAAAGGGGGCCCCC * MD:Z:4^ATTTTTTTTT0T3 NM:i:16