1@SQ SN:1 LN:247249719 2@CO Quality values: 30=?; 15=0; 40=I; 0=! 3@CO Reference starting at 10015: TAACCCTAACCCTA 4@CO ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS 5@CO Basic Read: AATAA CTAGA T AGGG 6@CO Just Matches: MMM MMM M M M 7@CO Reference: TAACCCTA ACCCT A 81:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AAT=ACTAGATAGGG I00?00III??IIII XN:Z:No Mismatches 91:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AA=GACTAGATAGGG I00I00III??IIII XN:Z:1 mismatch clipped from front 101:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AA==GCTAGATAGGG I000?0III??IIII XN:Z:1 mismatch not clipped, under filter limit 111:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AATAG===GATAGGG I000I0III??IIII XN:Z:1 mismatch - filtered - over quality limit 121:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AATAACT=GAAAGGG I000I0III??IIII XN:Z:1 mismatches, 1 clipped from back so last op is M 131:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AATAACTAGGAAGGG I000I0III??IIII XN:Z:2 mismatches, 2 clipped from back so last op is I 141:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AATTTCTAGATAGGG I00?00III??IIII XN:Z:mismatches from front so first op is D 151:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AATTTCATGATAGGG I00?00III??IIII XN:Z:mismatches from front so first op is I 161:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AATATCAAGTTAGGG I00?00III??IIII XN:Z:3 mismatches, no clips, but filter quality 171:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AATATCAAGTTAGGG I000000II!?IIII XN:Z:3 mismatches, no clips 181:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AATTAGGGGAAAGGG I000000II!?IIII XN:Z:clip all but one 191:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AATATCATGATAGGG I000000II!?IIII XN:Z:clip from start clips past where end was processing 201:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AAATTGATGTATGGG !!!!!!!!!!!!!!! XN:Z:clip entire read 211:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AAGGGGTTGAAAGGG I000000II!?IIII XN:Z:clip from both ends to same operation 221:1011:F:255+17M15D20M 73 1 10013 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 NNNNNNNNNNNNNNN I00?00III??IIII XN:Z:All N's - not a match/mismatch 231:1011:F:255+17M15D20M 73 1 100 0 3H2S3M2D3M1I1M3N1M1P1M3S = 10011 0 AAAAAAAAAAAAAAA I00?00III??IIII XN:Z:Reference all Ns 24