[mkreitzman@mkreitzman01 misopy-0.4.7]$ samtools view /projects/mkreitzman_prj/expression_quantification_testing/testing/test_data/strand_specific/JAGuaR_rev_87647/A08586_gr3.neg.bam | head HS13_70:4:2106:17314:23857 99 1 14212 0 100M = 14349 237 CTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACGGCCCTTCTCTCCTCCCTCTCATCCCAGAGTAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGC CCCFFFFFHHGHHJIIJIJIJJIJIJJJIHGJBHGGGIFGHGIIGHGIJJICHGCDHGIHEFHH??).??CCC>@ACACDCDADBDCDDDDDDBDBDDCC X0:i:3 X1:i:2 MD:Z:36T29A33 RG:Z:125843 XG:i:0 AM:i:0 NM:i:2 SM:i:0 XM:i:2 XO:i:0 XT:A:R XS:A:- HS13_70:4:2106:17314:23857 147 1 14349 0 100M = 14212 -237 CGAGAAGTTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCATTTTCTCTGGAA DDDDC@?;3CDDC?A@CDFED@FFHHEFGHIIGGGIHFAGCGJJIHC=DBDGJIHEGAGGGIIGGGAFAGEEGGIIHGJIHGGIGC@BFDFFDDDDBCB@ X0:i:3 X1:i:4 MD:Z:5C81G12 RG:Z:125843 XG:i:0 AM:i:0 NM:i:2 SM:i:0 XM:i:2 XO:i:0 XT:A:R XS:A:- HS13_70:4:1203:12112:172551 99 1 14354 0 100M = 14483 229 TTTTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTC CCCFFFFFGHHHHJJJIJJJJIJJJIJJJJJJJJJJJIHIIJJJIJHIJIDHHIIJIJJIJIJIIIJJJIIIIJJIHHHHFFDABEDDDDDDCDDDDDDD X0:i:3 X1:i:0 XA:Z:9,+14467,100M,2;1,+14354,100M,2; MD:Z:0C0G98 RG:Z:125843 XG:i:0 AM:i:0 NM:i:2 SM:i:0 XM:i:2 XO:i:0 XT:A:R XS:A:- HS13_70:4:1302:17329:22569 99 1 14356 0 100M = 14503 247 TTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTT CCCFFFFFHHHHHJJJJJJJJJIGIJJJJJJJJJJJJJJJJJJJGIJIGGIJJJJJJIJHJJJJIIJJJJIIJIHDHHHHFEFFDDEEEEDDDDDDDDDD X0:i:3 X1:i:4 MD:Z:100 RG:Z:125843 XG:i:0 AM:i:0 NM:i:0 SM:i:0 XM:i:0 XO:i:0 XT:A:R XS:A:- HS13_70:4:2101:9924:149977 99 1 14360 0 100M = 14502 242 CATCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGA CCCFFFFFHHHHHJJJJJJJJJJIJJJJJJJJJJJJJJJJHIJJHIIJJJJJJIJHIJJJJJJJJJJJIGHIJJJHHEFCDFFEEDDDEDDDDDDDDCDD X0:i:3 X1:i:4 MD:Z:100 RG:Z:125843 XG:i:0 AM:i:0 NM:i:0 SM:i:0 XM:i:0 XO:i:0 XT:A:R XS:A:- HS13_70:4:1302:1910:133080 99 1 14372 0 100M = 14448 176 CTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACTGTGGCGC @@@D7DABFAFFFFIIBF?:AFFDFEFEHHF@?EFEF@GIC4BB@BGIEFGGI@FIIFFEBFGIFFEFFIICC>EE;A?DDDD@63;;>=BBBBA>G@FEAEHGG@FH>@CC)(-5=<8;=5,(,389?CB0))9@BBB@## X0:i:4 X1:i:0 XA:Z:X,-155255238,100M,2;9,+14511,100M,2;1,+14398,100M,2; MD:Z:1G64A33 RG:Z:125843 XG:i:0 AM:i:0 NM:i:2 SM:i:0 XM:i:2 XO:i:0 XT:A:R XS:A:- HS13_70:4:1101:4495:55214 99 1 14399 0 100M = 14462 163 TTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGG CCCFFDFFHHHHHJJJIJJJJJGJJIJJJJJHIHIIJIHJJJJJJJJJJJJJJJJJJJJJJIJJJJJHIJHHFFDCDDDDDABDDDDDDDDDDDDDBDDD X0:i:3 X1:i:1 XA:Z:X,-155255237,100M,1;12,-91127,100M,1;9,+14512,100M,2; MD:Z:0G99 RG:Z:125843 XG:i:0 AM:i:0 NM:i:1 SM:i:0 XM:i:1 XO:i:0 XT:A:R XS:A:- HS13_70:4:1108:4042:53319 99 1 14400 0 100M = 14466 166 TTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGA @@@BBDFFGGHHFIIIJJJJJGIJE>HHJDHEDEDFGGGIIIJJFGDEAHGIIIHIIGGIJIJIIJJJJJHHFDD<@B?BCD8?AC@@BDDD15B>86=8??BB<