ad6ef3b792cf6a41a1a01191eee9d73aa68c9504 max Tue Jan 26 06:49:35 2021 -0800 update chromToUcsc to work with BAM files, refs #26839 diff --git src/utils/chromToUcsc/tests/expected/mm10.ebi.sam src/utils/chromToUcsc/tests/expected/mm10.ebi.sam new file mode 100644 index 0000000..0c7c492 --- /dev/null +++ src/utils/chromToUcsc/tests/expected/mm10.ebi.sam @@ -0,0 +1,150 @@ +@HD VN:1.5 SO:coordinate +@SQ SN:chr1 LN:195471971 +@SQ SN:chr10 LN:130694993 +@SQ SN:chr11 LN:122082543 +@SQ SN:chr12 LN:120129022 +@SQ SN:chr13 LN:120421639 +@SQ SN:chr14 LN:124902244 +@SQ SN:chr15 LN:104043685 +@SQ SN:chr16 LN:98207768 +@SQ SN:chr17 LN:94987271 +@SQ SN:chr18 LN:90702639 +@SQ SN:chr19 LN:61431566 +@SQ SN:chr2 LN:182113224 +@SQ SN:chr3 LN:160039680 +@SQ SN:chr4 LN:156508116 +@SQ SN:chr5 LN:151834684 +@SQ SN:chr6 LN:149736546 +@SQ SN:chr7 LN:145441459 +@SQ SN:chr8 LN:129401213 +@SQ SN:chr9 LN:124595110 +@SQ SN:chrM LN:16299 +@SQ SN:chrX LN:171031299 +@SQ SN:chrY LN:91744698 +@SQ SN:chr5_JH584299_random LN:953012 +@SQ SN:chrX_GL456233_random LN:336933 +@SQ SN:chrY_JH584301_random LN:259875 +@SQ SN:chr1_GL456211_random LN:241735 +@SQ SN:chr4_GL456350_random LN:227966 +@SQ SN:chr4_JH584293_random LN:207968 +@SQ SN:chr1_GL456221_random LN:206961 +@SQ SN:chr5_JH584297_random LN:205776 +@SQ SN:chr5_JH584296_random LN:199368 +@SQ SN:chr5_GL456354_random LN:195993 +@SQ SN:chr4_JH584294_random LN:191905 +@SQ SN:chr5_JH584298_random LN:184189 +@SQ SN:chrY_JH584300_random LN:182347 +@SQ SN:chr7_GL456219_random LN:175968 +@SQ SN:chr1_GL456210_random LN:169725 +@SQ SN:chrY_JH584303_random LN:158099 +@SQ SN:chrY_JH584302_random LN:155838 +@SQ SN:chr1_GL456212_random LN:153618 +@SQ SN:chrUn_JH584304 LN:114452 +@SQ SN:chrUn_GL456379 LN:72385 +@SQ SN:chr4_GL456216_random LN:66673 +@SQ SN:chrUn_GL456393 LN:55711 +@SQ SN:chrUn_GL456366 LN:47073 +@SQ SN:chrUn_GL456367 LN:42057 +@SQ SN:chrUn_GL456239 LN:40056 +@SQ SN:chr1_GL456213_random LN:39340 +@SQ SN:chrUn_GL456383 LN:38659 +@SQ SN:chrUn_GL456385 LN:35240 +@SQ SN:chrUn_GL456360 LN:31704 +@SQ SN:chrUn_GL456378 LN:31602 +@SQ SN:chrUn_GL456389 LN:28772 +@SQ SN:chrUn_GL456372 LN:28664 +@SQ SN:chrUn_GL456370 LN:26764 +@SQ SN:chrUn_GL456381 LN:25871 +@SQ SN:chrUn_GL456387 LN:24685 +@SQ SN:chrUn_GL456390 LN:24668 +@SQ SN:chrUn_GL456394 LN:24323 +@SQ SN:chrUn_GL456392 LN:23629 +@SQ SN:chrUn_GL456382 LN:23158 +@SQ SN:chrUn_GL456359 LN:22974 +@SQ SN:chrUn_GL456396 LN:21240 +@SQ SN:chrUn_GL456368 LN:20208 +@SQ SN:chr4_JH584292_random LN:14945 +@SQ SN:chr4_JH584295_random LN:1976 +@RG ID:S10192020TN9 SM:S10192020TN9 PL:illumina +@PG ID:bwa CL:/MG/SHARED/PIPELINES/RESEARCH/RH7/1.0/sentieon-genomics-201911/libexec/bwa mem -M -R @RG\tID:S10192020TN9\tSM:S10192020TN9\tPL:illumina -t 30 -K 10000000 /MGMUST1/SHARED/RESOURCES/MOUSE_Ensembl_Release_92//GRCm38.fa S10192020TN9_R1.AT.fastq S10192020TN9_R2.AT.fastq PN:bwa VN:0.7.17-r1188 +@PG ID:sentieon-Realigner CL:/MG/SHARED/PIPELINES/RESEARCH/RH7/1.0/sentieon-genomics-201911/libexec/driver -r /MGMUST1/SHARED/RESOURCES/MOUSE_Ensembl_Release_92//GRCm38.fa -t 30 -i S10192020TN9.deduped.bam --algo Realigner -k /MGMUST1/SHARED/RESOURCES/MOUSE_Ensembl_Release_92/mus_musculus.indels.vcf S10192020TN9.realigned.bam PN:sentieon-Realigner PP:sentieon-Dedup VN:sentieon-genomics-201911 +@PG ID:sentieon-Dedup CL:/MG/SHARED/PIPELINES/RESEARCH/RH7/1.0/sentieon-genomics-201911/libexec/driver -t 30 -i S10192020TN9.sorted.bam --algo Dedup --rmdup --score_info S10192020TN9.score.txt --metrics /MG/SHARED/ANALYSIS/MANGO/mango.prd/publish/files/2001603_546/2001603/DNAseq_Pipeline/S10192020TN9.dedup_metrics.txt S10192020TN9.deduped.bam PN:sentieon-Dedup PP:sentieon-sort VN:sentieon-genomics-201911 +@PG ID:sentieon-sort CL:/MG/SHARED/PIPELINES/RESEARCH/RH7/1.0/sentieon-genomics-201911/libexec/util sort -r /MGMUST1/SHARED/RESOURCES/MOUSE_Ensembl_Release_92//GRCm38.fa -o S10192020TN9.sorted.bam -t 30 --sam2bam -i - PN:sentieon-sort PP:bwa VN:sentieon-genomics-201911 +@PG ID:sentieon-ReadWriter CL:/MG/SHARED/PIPELINES/RESEARCH/RH7/1.0/sentieon-genomics-201911/libexec/driver -r /MGMUST1/SHARED/RESOURCES/MOUSE_Ensembl_Release_92//GRCm38.fa -t 30 -i S10192020TN9.realigned.bam -q S10192020TN9.recal_data.table --algo ReadWriter S10192020TN9.recaled.bam PN:sentieon-ReadWriter PP:sentieon-Realigner VN:sentieon-genomics-201911 +@PG ID:samtools PN:samtools PP:sentieon-ReadWriter VN:1.11 CL:samtools view -h S10192020TN9.recaled.bam +A00354:376:HN3JLDSXY:3:2110:16875:25238 163 chr1 3000148 60 4S93M = 3000151 93 TTGTCTCTATTTCTTTAGGGGAAATGGGACTTTTAGTCCATGAATCTGATCCTGATTTAGCTTTGGTACCTGGTATCTGTCTAGGAAGTTGTCCATT 6582=AECABBBFCBBAGFFFDBBBEFFDDCBBBAG@FDCBDCAAEBDBADCA;B@@@?EE0??AB<=@@?@@:;<8;=8>:7>==:?8:=7=;:88 NM:i:0 MD:Z:93 AS:i:93 XS:i:72 RG:Z:S10192020TN9 MC:Z:5S90M5S MQ:i:60 BI:Z:HHEHBKPRTUSOMQONPLPPPSTNPJOPSJNNNNPLNKOTRJQTPQPJRXQOMKRXROQLPQNNKONQMMNJONQSQPJNKPRLPSTLNLJLIINLK BD:Z:JJJD=AHJORRKPJOINMPKKPOHMMPLQLIOJJNMGJOPQMKPNQILLRSPKMLRPJONTNOJMPKLOPKMPLLPTKMHLKNORRSQINMFJMNOM +A00354:376:HN3JLDSXY:3:2110:16875:25238 83 chr1 3000151 60 5S90M5S = 3000148 -93 GTCAATATTTCTTTAGGGGAAATGGGACTTTTAGTCCATGAATCTGATCCTGATTTAGCTTTGGTACCTGGTATCTGTCTAGGAAGTTGTCCATTAGACA 897('5'88;7';:=??@B???5BCD>?@CB@@?(?3=)@'=2)2'%A?<''?(:99;0:0'=;'838,'-8 NM:i:3 MD:Z:68G12T1C11 AS:i:80 XS:i:21 RG:Z:S10192020TN9 MC:Z:97M3S MQ:i:60 BI:Z:HHJDELSSTPWUMQRNPPLUWSPNNPSLTNPSWQPRLNKOTTNPQPLPUULUTMORTKRTNNPQNPLTUNOMTRSLPSTNLPSTNNNNNOIORKJLDHHI BD:Z:JJLK9CKSRSPRPTNNNNNMQOMHHNPONQQQRSILMGJOPPINOMMSSQONQOHLPNLQJJOPJOONQJJONSPNRRQKPRRRKKLLKPNKPIHMKDGM +A00354:376:HN3JLDSXY:3:2420:26955:3427 83 chr1 3004210 60 97M3S = 3004100 -207 AACAAACAAGCAAACAAACAAACAAAAAACAAACAACAAAAAAACACACAAAAAAACAAACCTTTAAATTATAGGCATGGATAGGGAGAAGAAACCAGGC 65:664:8/,<:;'?<<'A??(;?)@@@5D6A?E6@EBBBBC8AFAFAFCCCCCCAFCCA>HCCBCCCCBCBDFHBCECDEC(B@B:?BAA?A?<1::99):8'8:9 NM:i:0 MD:Z:96 AS:i:96 XS:i:20 RG:Z:S10192020TN9 MC:Z:93M4S MQ:i:60 BI:Z:HHJDELPRSNRKONOPSSPNPSSSLTRSSSLTNNMNPPLNNOSJNNNNMQNPLQOOPONTONJOQPOQNPQRPLUOUJTTNLUWJQWQRSMLLJPPHHGN BD:Z:JJLK9CJORQLNHMJNOONINONNMMRPPPONQHLINNNGIOPKHMIIOJOONQKJPQRQMIMQNMPOKMJMOPNLOMNRKPOSOMTUQRJIINLOGGLK +A00354:376:HN3JLDSXY:3:1540:23891:2848 83 chr1 3005664 60 93M4S = 3005464 -293 TGCAGCCTATTGCTATTGCCTTTGGTTGTTCCCAAGAGGCCAAAGGTAAATTCCTATTCATAAAAATACCATGCACTTTAGACACAAAAGTCAACAA 2;987<>8:;=AA;=>ADC;?@BCBA69ACFFEBCF?9HGFCCDFEBCCCCEGHBCCEFCBCCCCCBAGFCEHFAHCCBDGAFAFCCCDEDC92856 NM:i:0 MD:Z:93 AS:i:93 XS:i:19 RG:Z:S10192020TN9 MC:Z:4S96M MQ:i:60 BI:Z:NIDKKOLSPTTQMTQUUOQMOUUNNUUNUTQPLOQQNNOPLOONNMQORQUSQLSPTQJTQNNORSQOPJSUOONMNPRPKOOOLPPPQLQFDHEHH BD:Z:PNJKOOLONQSTNPOQSQQOJQQPOQMNPPKOLNILJQPOLINJPONIOMOOPMONPKMONJJJPPLKPNRROHFNJNLIJFJHNLLQKLHD@DJJJ +A00354:376:HN3JLDSXY:3:1616:23457:1564 163 chr1 3006475 60 4S93M = 3006572 190 TACTCTACAGGCATCTAAGGAGTAGTTAGAGCAGCAGAAATAGTCTCCTCTATGGAAGATCACATAGACTTGTTATCCAATGCCCAATAGTTAGCCC 6475=A@DDGFGDBFC7BGFDG8AG@BAGDGGDGGD>DAAB@F?EBEDAE<2@;DB@EB@DAAA>=C@)>>@:<%?>??A7&>BB6C6C7CBCDGCCEHBAFCEEBCBCBAFDGCBAFCBCBCEHFAHEGCCCDGCDEE<2856 NM:i:0 MD:Z:93 AS:i:93 XS:i:21 RG:Z:S10192020TN9 MC:Z:4S93M MQ:i:60 BI:Z:GHDMNMJSSRRLOPLRTTQUUMROKQLOMQORPKQRQQTTQRQQQOQRQUVLRNJRTLSTTSQOKPQTRNKTSTSSTONNNSMOOPRNQOMJEHEHH BD:Z:JDKMJELOORPKKPMPPPOQNOLGMJJGMNNMPLIRNNOONONNOOIRNOLLKFMQMNOOOPLGMJSPLGNONNNQSPIGPOOKKQLQQKNH=DJJJ +A00354:376:HN3JLDSXY:3:1108:24343:17378 99 chr1 3006771 60 5S95M = 3006916 241 GGTGTAAAAAGAGTAACGGAATGGGAAAAAAAAAGAAAGAAAAAAGAAAAAGAAAAGAAAAAGAAAAAGAAAAAAAGCCCCCTTTTCCCCCTTTGATTTT 69378?BCCCHEHABCEBGE,CFGGECCCCCCCCHECCHECCCCCHECCCCHECCC?ECBBBGDBBBAFCAA@@@4;DBBBA><1<8>1<A@@B@-<,'A?DCD@BCEE7C@@BCA?BCA@A?D@DBFB@GBACDDFBBABDEBBBA@EBABDDABBBCC:8246 NM:i:1 MD:Z:0T95 AS:i:95 XS:i:0 RG:Z:S10192020TN9 MC:Z:5S95M MQ:i:60 BI:Z:DKDGIHMKLJMMNNTOTJULTQJRTNPPNSKONNJQNPLTTNQPRKQTQJTSNMPPMNNNJPLMNLPRNORLQSSWQJPNPQNJSTSUMRPSYQEGKLHH BD:Z:IIJHNMNLFMKNJSONOMOPRLOSSQMQQPKGJGMNQQOQQRTLLNOQLNPMHNMNLFIFLINLGNOMIMPOPPOPJLNINKFMOPROPQLRRGD?3B=)B3A?<0<;>'998<'066066 NM:i:1 MD:Z:63T32 AS:i:91 XS:i:29 RG:Z:S10192020TN9 MC:Z:15S78M4S MQ:i:60 BI:Z:HHKJGINRVLSVMVKUONNPSRPMNSTJRUMNQQPONQOMRLNQTQLRXROMSSRLPQOLQQSSTQMQONLPQORTKONLOORUQRNKNMNMIONMHHJM BD:Z:JJKJ=FFORPNSPOLMLHNNPOMMGLPNLQOIMJMPJLOJLMGKONKJQOIOPQOLOKJJILOQONNPJLLPLKLPNGMMGJLQOPJMFLHHMNPMGGLM +A00354:376:HN3JLDSXY:3:2568:1533:4053 147 chr1 3008284 60 15S78M4S = 3008147 -215 AAAACACTTTTTATTAGTAGAGGGTTTTTCAGTTTCTATGATTTTGTAAGCTTTATGTTGTTTTTGTTGTTCTTAATATCCAGCTTTAATCTAGTAG (83',1?::::%&9$:39;-8??><='25A?@3?6D?@BD3(@4BB?5AFFAA@AC:ACDBBBBD+BD;BD?BABBABDFECGG:BABBDF?:6466 NM:i:2 MD:Z:11G14G51 AS:i:68 XS:i:26 RG:Z:S10192020TN9 MC:Z:4S96M MQ:i:60 BI:Z:HHGHLLKMNNPSPPRNLRPPMQMMNNOTRJNMNTULSRSRQOOUTLPORPLNPSRTMTTMNNNTTMTTMTULPPQSSWSOJQQMOQRSYWLMEFLHH BD:Z:GGJDIGOKKLQQPPNJPNJNLOPPJJJQLMIOJQNNPRPSOJJQNOOONSNHNOQMNPMNIIIQNOQNOQNNMMNOOQPOLMTOKPQRTNID;LJJJ +A00354:376:HN3JLDSXY:3:1224:24279:15421 163 chr1 3009537 60 4S96M = 3009647 205 GGTGTTTTACTTTATCATGAAATATCTTGCTTTCTTCAACTATGGTGATTGAAAGTTATACTAGGTTTAGTATTCTGGACTGTCAAACAGATTCTGTAAG 69377:ABADCBBABFDBEDBBBABFCBE?CBBFCBFDACC@ADE?DC@ACB@@.>@?3?B0>DB<>(=B'0'18=>4<<;+6=;1:<<8<'(<:;278; NM:i:2 MD:Z:68G18G8 AS:i:86 XS:i:28 RG:Z:S10192020TN9 MC:Z:95M4S MQ:i:60 BI:Z:HHHHEHNPRNPOOQTQRRJQTNPSSQPNKOQNNLPNLRTMNRSJONNQXRKQTOMONQTSLNRLPNMNQLOQSQLPJOSJNJNKRTNMTMTUOILFHKJF BD:Z:JJHG9DEJQQKPKOPROQMKPIMNNRJOMQNOJOINNOPNHLOMOIIKRPMLQJOHMOPPOIMNQKMJONHLPQOJNQQMJNHLQRLQORNQONHKDILL +A00354:376:HN3JLDSXY:3:1224:24279:15421 83 chr1 3009647 60 95M4S = 3009537 -205 CCTTATGGCTTTTAGAGTGACTGTTAAGAAGTTATGTGAAATTCTAGGAAGTCTGCCTTCATATGTTACTTTGCCTTTTCCCATTTCAGCTTTTACACC ;,65'11=70'0:=@=?@.=DA7@?@AE*B9AABDDDFBBCCEHBDFGCDEEHEHGHCEFCBCEECBAHCCEHGHCCCEGGFCCCEFDHHCCB?77396 NM:i:1 MD:Z:4C90 AS:i:90 XS:i:30 RG:Z:S10192020TN9 MC:Z:4S96M MQ:i:60 BI:Z:JFJMNQJOLNNPRQQOPSLOOUNQQOQMOONQTSUPSMORQUVMSNPMOOKVOTOPLTQJSTSTMQRNLOUTOQLONUSPOJPOURKSRNQPPLEHHHH BD:Z:NLLMPOPRMIIOMJMIMPKHQNOOOOJONHNNOQMLONIONPMMLJPONHKLOQPPNPKMOOQNOOLHOJQSQPMHHPQKOMNIQMNPVQLJKC:GHJJ +A00354:376:HN3JLDSXY:3:1268:26820:6731 99 chr1 3010646 60 5S93M = 3010858 290 TATGTGTTTTTGGTTTGTTTGTTTTTTTTGTTTGTTTGTTTGTTTTTTCTGTTTCCTTTTCAGTTTTTTGGCTTTTGTGATCTGGATTTTTGATGGCT 64578C;CCCCFG.CCFACCFACCCCCCCFACCFACCFACCFACCCCCGDFACCGFD8CBFDG7BB*A6DE8@4;;099;)/,:;7 NM:i:0 MD:Z:93 AS:i:93 XS:i:31 RG:Z:S10192020TN9 MC:Z:15S78M2S MQ:i:60 BI:Z:HHMDEINOQPPMPONOKNMNKOMONOONOLNMOLNMOLNMNKNMONOOMQKONOMPNOOOMSOONOOOOLPOROOOLOORXRQKPTWQNNNJNTDIHK BD:Z:JJMK:ACMLLLOQLMILFLIMFKHHIJJJMGMJMGMILFLILFLIHHHNILGMINOJNIINOPGLIIIILOQNOJJMGJLRSJMPQRPIIHKJPKMNK +A00354:376:HN3JLDSXY:3:1133:18132:23187 65 chr1 3010703 60 4S96M chrY 18969108 0 ACGTGTTTTTTGGCTTTTGTGATCTGGATTTTTGATGGCTATCATGACCTCTGAATGACTAGGGAATCTTGGACCACATTGGGGGCCTCTACTAGCTGTT 6742<>BCCCCFGHDCC;FAFECGDFGECCCCCFECFGHDBCGECFEEFDGDFECCFEECAGFFDB)EBADEBBCBAA??BBA5@A><>:.396;;/:52 NM:i:0 MD:Z:96 MC:Z:59S41M AS:i:96 XS:i:21 RG:Z:S10192020TN9 BI:Z:HHGHEIMPQPPMPORONNKNNRWRPKPSXRNNOLQWKPNQRSQRSJRKNNQQKRUQKRKOSMQQTUQRQOLPTKNUPUSRLPQQQOMMPPRKKOHLKDHG BD:Z:JJLG=>IJLLLOQRNNIILFJKPQHLPQRPJJJMLRMOPMLOROQLJJOJLJMKPNMKKHLMPKPPNRINLPQLPQMNRPMPLLLQRKLIKMGKLQKJDJ +A00354:376:HN3JLDSXY:3:2420:15637:7028 99 chr1 3010766 60 3S55M1I41M = 3010867 195 TGACTTGGACCACATTGGGGGCCTCTACTAGCTGTTAGCTTGGCATTTGGTACCATGCGGGGGGGGGGGGGGAGGTGTCTCTGTTATGGTTATTATGGCC 6876:@EGEEFEEE:CFGGGGHFDGDBEDBHHDFACBHHDCFGHECC9FGABEFECFHBFFFFFFFFEEEEE*;D(;=C0./@:1%'>)'9787%68;<9 NM:i:4 MD:Z:81C2A0G10 AS:i:74 XS:i:25 RG:Z:S10192020TN9 MC:Z:94M5S MQ:i:60 BI:Z:HHKDEIKQVLOVPUSRKOPPPOMNPQSLOSLPRKNMQMPQNKONURROLPORMNUSKPSRQQQQQQQQQQQQTPQOOOLQQQKONQSJONMOPNLODIHG BD:Z:JJII()>-';'1(%:,>1'7-(9:2 NM:i:1 MD:Z:45C6 AS:i:47 XS:i:20 RG:Z:S10192020TN9 MC:Z:8S40M6S MQ:i:60 BI:Z:HHFHGMRSNQRRQONNPPRLNSLQQKOMQMPQOLONUSQNKONQMMUSKRPQQQQQOOOOPQQQTXROOOQMVUQROQTRQMORTRNPSJOLQOMIKKK BD:Z:JJLF@GNPORNNMRRJLILNILLRLLGMONTNOMPQRQOILOJKNNOPMKKQLKKKJIFIOKKKPQOIIINNNQOPJOPPONHLPPJOOMOPOPQMLLL +A00354:376:HN3JLDSXY:3:1216:10827:10473 147 chr1 3010853 60 8S40M6S = 3010775 -118 TTCAGATGATTATGGCCTGCACCTGTTATTCTGGCTGTTGTGGCCTGTTCTAGC @BC0<@)EAA@A7EFE/8GE@FGD;BA7)DGDE/0DA?:AC3A)=?*ADACEEBB@BB(5EEECC@?FA@BBFECEFBB?DDEBCGECFBBBDFCEEDACEEEGED<:966 NM:i:2 MD:Z:12T2T62 AS:i:68 XS:i:19 RG:Z:S10192020TN9 MC:Z:5S93M MQ:i:60 BI:Z:KGDKIPNQMQPPRMQMNPNTONNPOTNLRNJUNTMPOUNUUPTMNQOTLQNLPPNQOJMOLNNNJQKNQOJPLQPTRPMQNMSNSSOPPJAJJHH BD:Z:LMIIMORSQTPPNLPSQRRSQKKQQQPOMILNQQRTQNOQNMQRQQQMNJGNNNNMPLJONJOILLMONPKHMONPOLJNPONLQQTQGG?GJJJ +A00354:376:HN3JLDSXY:3:2420:15637:7028 147 chr1 3010867 60 94M5S = 3010766 -195 CGGTTATTCGGGCTGTTGTGGCCTGTACTTAAGCAGGAACGTCAAGCAGAATTGAGGGTAGGGGCCCAGCAGTGGGATAGGTGGTGAGATAGGTACTAC 7(:8780)9(=?7=;/:;1=?>@>>;:B><>?CA?BC?>&BBC@AECADA@ACEBDDCA=DEEGFFECGECDDEEFBACEDDEDDFCFBACEC?79436 NM:i:3 MD:Z:1T7T29A54 AS:i:82 XS:i:0 RG:Z:S10192020TN9 MC:Z:3S55M1I41M MQ:i:60 BI:Z:FGGJOMRQKPMPNTMTTOTMNPNTLQNLQPOQOJMOLMNMKRLORPJPLRQTRPMQMLRMQQMNPOJQOJNOTQOQSRMMOTMOSQQRUTOOLLEFKHH BD:Z:MMLLNNPQPPSVSOPRONRSQRRNOMHOOOONQMKPOMJOLLMONQMJOPOPOKJNONLJNNQPKPMNQMIMQNNQNLJOLPOLPMKTROMPJC:KIJJ +A00354:376:HN3JLDSXY:3:2161:8567:31140 99 chr1 3011140 60 5S95M = 3011195 131 TTTGTACTTTTTAGGCATTCTTAATGTTTTTATTTTCCCATCTCCTCCCTAATTAGAGTCATTCTGGTTTTTTTTTTACATTTTTGCAATTAGATAATTT 65577?DDCCCCBHGHECCGDCBCCFACCCCBCCC:GFFECADGFDGFFDBCCCBHEHAF9BBFCEF?AAAA@@@@4&AA(2=1(,,=:9(7796/17(6 NM:i:2 MD:Z:72C7T14 AS:i:85 XS:i:22 RG:Z:S10192020TN9 MC:Z:76M MQ:i:60 BI:Z:HHHEELLPQPPPQMQOTRQLPOPQPKOMOONPTRNNMPQTRQPPPMQPRNSQQRQMVPOLSSRMQKPONOOOOOOOOQMUSROOOLOTTPQOIRSOJJKH BD:Z:JJGJ:CKIQLLLPOQPRQONJNMMMMGMJJJOPPJJNONPQRILOIKNNJLOOONMMKGJOQONILOJLIIJJJJJJOONRPJJJMQSPNNMLLPMLLMG +A00354:376:HN3JLDSXY:3:2161:8567:31140 147 chr1 3011195 60 76M = 3011140 -131 ATTTTTGTTTTTTTTTTACAATTTTTAAATTATTTAATTTGCACTCTTCTATTCCCCTCTCTGTTACTCACGTCAG <'<12'?'>>>>?(?@?(-@34@@@?)@A(@)A)4*A6BDG.)/+/BD?ABBDFFFGDGDGDDBA@GDE??;6866 NM:i:8 MD:Z:3C1G11C2T5C5G0A41A0 AS:i:44 XS:i:24 RG:Z:S10192020TN9 MC:Z:5S95M MQ:i:60 BI:Z:JHHHTUMONNNNNNNPQOLRQOONPPORPPSPNPPQPNTTONNOULTULSPTSPPPOUOUNUNQRPQSPNHAKDHH BD:Z:LGGGQNOJJJJJJJJOLGMPOJJJOOJPNNNNINNONIPRPIHLNOQNNPNOOJKPKMKMPNOPMJNNJEF>IJJJ +A00354:376:HN3JLDSXY:3:1663:5556:30843 99 chr1 3011583 60 3S89M5S = 3011583 89 GCCTTCTATAGTTCAATCACTTATTTAATGGCTTATGTATTAAGAATTGAGAAAAACAATACTGCCAAGAACCAGCTTCTGCTAGGAGAGGGACTAA 6:859DCBCBHACGECCGEEDCBCCCBCCFGHDCBCFABCCBCHECCCFEHECC8CEECBADCEGEDAF9ACCBEE@?.@BC>;8@4@<>=<337/6 NM:i:0 MD:Z:89 AS:i:89 XS:i:21 RG:Z:S10192020TN9 MC:Z:5S89M5S MQ:i:60 BI:Z:HHGGEGPTVUNPNMSUPQRONOPTQOQPQKONROPSKOQSQPPLVTQRLRPVUOOONUUQTMOKPNUUMVUNNUOQROMQKPRSMQSOUOPOPDHLJ BD:Z:JJOHBFFMRRPJNPPPNROLINMNNIOOONPQNOOPMFKOONNNMOMNLKKNQIIINMPNONHLPQPPNMPOPQQTNOOJMQNMNQQLMKOJOIFJL +A00354:376:HN3JLDSXY:3:1663:5556:30843 147 chr1 3011583 60 5S89M5S = 3011583 -89 CTGCCTTCTATAGTTCAATCACTTATTTAATGGCTTATGTATTAAGAATTGAGAAAAACAATACTGCCAAGAACCAGCTTCTGCTAGGAGAGGGACTAA =:=<=8;>9:97<;(<89<=8?;;<<<<>1@AC:>>?AB?@@?@AD@@@CDBEAAAA?EAAA@GDGFEBCFB@FECGGBDGDGGACEFCFCEDD79456 NM:i:0 MD:Z:89 AS:i:89 XS:i:19 RG:Z:S10192020TN9 MC:Z:3S89M5S MQ:i:60 BI:Z:HNHJHQSJRRRNMTQKQWQNNLPSPNPPRRUMPLPSRTLSQQQOQMQPTSQPLNNNMNKQSQNNTNOKNPLMNOJQPLTUNTPLSNPQRROSOFEFJHH BD:Z:NPNNMPMMPQNKQRMNQSMKHPPPOKOOPRQRTOOPRNOPOOOOJOPOQPMINHIILFLOOKGPRQPMOJOMKOKLRNPMPRSMMKQNLOMOKB:KLJJ +A00354:376:HN3JLDSXY:3:2327:21784:36213 99 chr1 3011963 60 4S96M = 3012017 149 CGCTTATATATACTTAAACATAGCAAATGGATTCAGAGATTTGTCTGCCTTTGTAAGCACTGACAATAAACTAGCTATGTGGGATCTTGCTCTTAGATCA 64:59?BBCBCBEDCBCCEECBHHECCCFGECCGEHEHECCCFAGDFHFDCCFABCHHEDCEDD)BB@A6CB?EEA>?-=BBA><@<;=7/>7&1<<=>@<4A=@BA'A0B@C2BC>DCAB@BDC<9?,?>5?><<887<:9889-8-)?==?:*A;@@@?AACFADGDDABDGEFECBDEEECCBCC:GCCCBCAHEFCEGFCBAHBAHCBDFEEHCEGFCBCEEDE82856 NM:i:0 MD:Z:95 AS:i:95 XS:i:0 RG:Z:S10192020TN9 MC:Z:4S96M MQ:i:60 BI:Z:JJFHJMOOLNNQWTPKTQOOPSRQOQTQUVMUVOUMTXVOUNNQSOPUNOQTQTSQPNPPMOPQJXTOJTRNMRNMPSMMJULUTPKUUTWLUGHHEHH BD:Z:INLGHMKHMIIPRQPNPOOIMPSOJOPOPMNPMPMNOQMPPONNLHMNNINNMOORNINNLGKLNRQPNPLHNKFMMLKOKMNPQQORRTPLJE?DJJJ +A00354:376:HN3JLDSXY:3:2253:18014:13150 113 chr1 3013295 60 5S91M4S chr17 53515722 0 GGACGTGCTGGGAATTGAATCCAGGTCCTCTGAAAGAGCAGCCAGTACTCTAAACTGCTGAGCCATTCCTCTAGCAAGAATGATACTATTTTTTATACCC 9-5%)'<=:1<7;;<>@=>A*B@BBBDECFCE*BCFCGECGGFDEBAHEHBCCAHEHHEGDHGFCCEGHEHBDHFCDGCCEGCBAHBCCCCCCA@82996 NM:i:0 MD:Z:91 MC:Z:96M4S AS:i:91 XS:i:43 RG:Z:S10192020TN9 BI:Z:IEHGKPMKSQOLQPUSMRXTPKNNKTQPVOSMOOQQRPKROPKOMROPVMQONONUPNRPQNPKPTTQOUMSQPLNQLRRRQSQOMTQPPPQRSNHHJHH BD:Z:MHGLJQROOMONPOQPOPRQPMKPLQQLNPONINILMPLMPOLHNKGLNMNIKFORSPOLMPOMOQQQLNNMNQLMHMOROROKGNQPLLLLOLG?HIJJ +A00354:376:HN3JLDSXY:3:1137:12518:1658 65 chr1 3014155 60 4S87M9S chr7 46002588 0 AGCTAACTCTCATTAAATAAAAACAAATTAAAAGTGATTGAAGGCATATTTTTCTCTTTGGGATTTAGGATGTCACCGGAAAAAAAAAAAGATTTGGCAT 6::58@DDGDGEC;BCCCBCCCCEECCCCBCCCHAFECCFECHGHECBCCCCCGDGDCCEFF:BBBAFE+)->D5B)&CA?>=11';'0'-38069)+'6 NM:i:2 MD:Z:65C7T13 MC:Z:3S97M AS:i:77 XS:i:24 RG:Z:S10192020TN9 BI:Z:HHJKIKMPSRRTSRQQNPSPNONNTUOPRQPNOMNNRXQKQTLPOTSTTROOOMQQQOOLPQTXROQMQTXKOLSPNMRTUOOOOONNNNLTTNJGIHNL BD:Z:JJQK@FKIOLORSQONINONJIHMLPJOPOOJJOHJKQOLKPNPPQPNOOIJJNILINILOKPQOINMPPQNGKPMPPQQQJJJJJJJIIMLPNHJMNPO +A00354:376:HN3JLDSXY:3:1421:14922:27774 163 chr1 3015251 60 2S97M = 3015363 207 CTGTCCATCCTTTTGTCACAGCTCCAAATTTTGTCTCTGTAACTCTTTCCATGGGTGTTTTGTTCCCATTTCTAAGCAGGAGTAAAGTGTCCACACGTT 6682=CCBFECBBBE@FDDDGGCFE)B8BBBBE@FCFCD?5ACBEBAADDB@CDD>C>)@@B=?BAA@>=>A=%1A@/89;?8,8><;:::%68 NM:i:1 MD:Z:94T2 AS:i:94 XS:i:79 RG:Z:S10192020TN9 XA:Z:9,-94173011,97M2S,4; MC:Z:95M5S MQ:i:60 BI:Z:HHDHBJTTSQOOOOLNKROTNPQPOTTNPQNNKNKPPPJNQPMNPPNNMPTRJPQOOONNNKNMLOQTSQOLPRPLPTNPSONQPNLNNMJMRLPIGHG BD:Z:JJJD=GLRURMPKJMFJOLMPSLKNPQJOPJJMGJILILFKNNHLHNIOPQRNPLKJGMJJMGMOPOQRPJOJNOOUTQRRMIMPKQJKHKOPLLJLGJ +A00354:376:HN3JLDSXY:3:1421:14922:27774 83 chr1 3015363 60 95M5S = 3015251 -207 TGTATTTAATGCATTTGGCAAGTTGTATCTTACATCTTGGGTATCCTAAGTTTCTGAGCTAATATCCACTTATCAGTGAGTACATATTGTGCGAGAGTAG 896616688;>=/;<'?BA?@A?AB&@BFA@?DB9GBDEEDBCEGHBCDECCEHEGDHHBCCBCEGFAHCBCEFBEEGDEBAFCBCCEEEHBGCD:6466 NM:i:0 MD:Z:95 AS:i:95 XS:i:77 RG:Z:S10192020TN9 MC:Z:2S97M MQ:i:60 BI:Z:NFMJJLMNQTOJPNUUNPLOONUUMTXVMQROKXVMUURNMTXTQMQOONOUVORQQPLPQSTXSOOOLPTXQKOOSPOLQNJSTQUUQVVPRPKEFLHH BD:Z:KLMLGMMNPQPMOJQQRQMOIOQNOPRNONKFMQMNPPNONOQPPMNOINIPLONLMSMNOOOQQPJHOOPRLMHKNKHOKFMOOOROOUTQMFD@@@?ED@CAA9>A;B?11A>;>7;;;>'/9?>7<6,6; NM:i:0 MD:Z:93 AS:i:93 XS:i:88 RG:Z:S10192020TN9 MC:Z:96M4S MQ:i:40 BI:Z:HHHKIGNOMPPPNUOPTOMTRQNKNMPPNNNPJOQJNKPNNNNNLOTOOKOSWKPONOOPLPQPOQMNLNLRTNLUWQRNPNNQJMTRSKOLLHHHH BD:Z:JJNK?ECMOILRSQQSRLOPQOHKELOOJJJONQMLFJINIIIINNPLIMPQRNPKMJJONTNMPOKOMGKPQKONSTPRRLKMMQSTQOQJIDGDG +A00354:376:HN3JLDSXY:3:2277:6271:22842 83 chr1 3016591 40 96M4S = 3016422 -265 CACAATTGCACTGTAGTACAGTTTTAGGTCCGGCATAGTGATTCCACCAGAGGTTCTTTTATCCTTGAGAAGAGTTTTTGCTATCCTCGTTTTTTTAGGC 9':66'9=;'-<=:=>;;A@A?(?2;CB8E@DFEBACDDFBCEGFAGFDGDFEC@DA@@@1?CA:>A5B5=8)A:10::=>9$9?''>98901882,37 NM:i:1 MD:Z:81C13 AS:i:90 XS:i:90 RG:Z:S10192020TN9 MC:Z:96M4S MQ:i:0 BI:Z:HHMIELSSMQSQQKOQLNQLTNNMNNPLPNKOLQNTRSLNNQWQLOTONUNUOQONMQONNPSQOMNKROVTLUONMNNNKOQRSQRRQLMKLKJJHEHG BD:Z:JJOI:CKPOSPNKMGKMGKNMPFKHIONQKKPPQPRQOMGIKQONNPLPQQNLQKMOJOJJOPSPKOMLLNQOOLHNKJKNRONQTRTTPJLIIHHGJDJ +A00354:376:HN3JLDSXY:3:2404:21531:1047 83 chr1 3016619 0 96M4S = 3016595 -120 TCCGGCATAGTGATTCCACCAGAGGTTCTTTTATCCTTGAGAAGAGTTTTTGCTATCCTCGTTTTTTTGTTATTCCAGATGAATCTGCCGATTGCCAGNC 8)69;97./;'-;;>@?')B@C@BB4*E(AA@ADFGBDFCFCDGDECCCCEHHBCEGHEBECCCCCCEECBC;EGFDGCEGCCEHEHGBGCCEGD<56#6 NM:i:0 MD:Z:96 AS:i:96 XS:i:96 RG:Z:S10192020TN9 MC:Z:5S95M MQ:i:0 BI:Z:MKFGKFPOMORQPTTPOOPKQQNNNUVMOOQTXTQMUSQQMOQQONOOOUUQMTWTPOSMMNOONNUUMPTQTTPJQQSRLQWUOUOROSRWVNJAHHHH BD:Z:NNMONLNKGKOROQQPJKPMJMKPOQNOJINOQPPNPOLINNILHNIJJPRSLNPPPKQNNIIIJJQNOOPOQQOKHQQPNOQMPSRRQUQSSMG@JJJJ +A00354:376:HN3JLDSXY:3:1110:32380:23030 163 chr1 3016851 40 5S95M = 3016987 231 GCTCTTGAAATCTTCTTTAATTTCTTTCTTTAGAGACTTGAAGTTCTTATCATACAGATATTTAAATAATTAATTATATTCACGCCAAGGTATTTTATAT 6:68:@DDBBBF2BFCBBABB+BFCBBFCBBAGDGDDCADDAF?AEBA?ADB@?BB;B(2(??&>(>%'=(<1<(;'%:(7&:8>>':-)18983870&7 NM:i:7 MD:Z:58C1C1T0C7G1G9T11 AS:i:60 XS:i:58 RG:Z:S10192020TN9 MC:Z:95M4S MQ:i:42 BI:Z:HHKJGIKSVPRRQOMPNNPPPQNLPNNLPNNPLUOUJNNKQTLNMLPNQTQRRTMUOVXSSQNPPNPSQPRPPPQPSSSQLROMTMTTLOMOQNJJJMMM BD:Z:JJKJ;)0;;<>)C??A75*?>CBEAA=EGFEBBDFA?CB7CCEGD?:AB?@A?>C@ACCA7FBBA>ED6DFFHBGDGDEEFGAFDGAHCEEEHBDEBAGHEGCCCCBDEEFFGCCEHHCEGE@77556 NM:i:1 MD:Z:6T88 MC:Z:96M4S AS:i:90 XS:i:85 RG:Z:S10192020TN9 BI:Z:KJNNKJKKSMPLRMPLOMURLOOMROLRSUNUSMRTSNNMSNRNUNQQQOPUPLNKPKNLTTKVLROMQNQORRQNOPSNOTQORQUURNVVQKHEDJHH BD:Z:MLNPNHFOOPSMMKPKHOQLMOIOLGMPRMNPONOOLJONLJNQQNLJMHLPNIELIJGNPMKMNMIOLKQQPSNHHMLILPNORORTVQSSPID:KLJJ +A00354:376:HN3JLDSXY:3:1555:11677:22498 99 chr1 3017615 60 3S96M = 3017694 179 TCGTTTTTGCATCGATATTCATAAGGGAAATTGGTCTGAAGATCTCTATCTTTGTTGGGTTTTTTTGTGCTTTAGGTATCAGAGTAATTGTGGCTTCAT 69429@BCFHECGBECBCCGECBCHGG>CCCCFGAGDFECHECGDGDBCGD9CFACFGG@BBBBBBE?DFBA@?ED=>?:AC?A1;;;:77;<<76:90 NM:i:0 MD:Z:96 AS:i:96 XS:i:86 RG:Z:S10192020TN9 XA:Z:12,+119125311,3S96M,2;10,+38026143,3S96M,2;11,+66195880,3S96M,3;14,+8811795,3S96M,3;12,+109261749,3S96M,3; MC:Z:100M MQ:i:47 BI:Z:HHGHDINPNQVTRNTXSSQLRSSQLQQSUOPQLPNKQKQTLUWQQPQSTRQOOLONLPQONOOOOOLOOPROOQMQORTRSOVPORPPQKNMLKMHFLL BD:Z:JJLG@AFJOSUTTPRQOOONPQNMMPLQQJOPMPKKILKPNMQRIKHKORIOJLFLLOKJLIIIIILFIPMOJONQKLPSPQNLHLOOOLEHNOLLLMO +A00354:376:HN3JLDSXY:3:1555:11677:22498 147 chr1 3017694 47 100M = 3017615 -179 AGTAATTGGGGCTTCATAGAATGAGTTTGGTAGAGTACCTTCCGTTTCTATTTTGTGGAATGGTTTGTGAAGAACTGGAATTAGGTCTTCTTTGAAGGTA 867888:(((??')>98.=0:<7<)<<>@@+BBE@A=FF1AAEB3@A?@@@?@;>@C>?>?>A@>9?1A>AA?<:9':=;;&>>'=):=%5:87=<9 NM:i:2 MD:Z:76G12T7 AS:i:87 XS:i:92 RG:Z:S10192020TN9 MC:Z:94M5S MQ:i:47 BI:Z:HHDHEFQQWVNVPOONMKNMLRNNMNLOTOMNNQTPJNMKONQNNLPRTRPSQOQTKONKNMPSQKQTMUXQRNPMMNPSQLOTRJONNPVOKNOSMFJM BD:Z:JJIFADGLPSQOMHJFLLFLNOOFKIOPQMOJJLPNMFLLOPMNIMILPPOPPJOPNGMMGMOPPMLQONRSPRTRLPOQQPQRSORMKMRRNPOPMKNN +A00354:376:HN3JLDSXY:3:1362:20726:13964 83 chr1 3018659 47 94M5S = 3018466 -287 AGAAGATATATTCTTTTGTTTTAGGATAAAATGTTCTGTAGATATCTGTCAAGTCCATTTGTTTCATCACTTCTGTTAGTTTCACTGTGTCCCTAGACT 8;17-'7889:=-'11?@?3?2;CD@?AAAACDB:GDDA?GCBCEHEEEFCDEEGFCCCEECC=FCEFAHCEHEECBDECCEFAHEEEEEGGG?:83:6 NM:i:0 MD:Z:94 AS:i:94 XS:i:84 RG:Z:S10192020TN9 XA:Z:Y,+28997546,5S94M,2;3,-104198151,94M5S,2;13,-84970936,90M9S,2; MC:Z:3S97M MQ:i:40 BI:Z:JFHJMPPRSPTULOOUUNOOQSNPRTQOORSUNUVOUMSQRTTXVOUKRLOOKSPJPNTTMOUQJXRNNMUUOUMQROMNTQNOOUPVLUSRLMGEHHH BD:Z:GLLGQNNNNNPNOJJQNOJJOMKPSPOJIOQMNPMPMNLIROOQMPNLKLNGJOOMNIPMNIPLNRLJHOQNQMMMKHOIPKIGQONPNSNQJD=HEJJ +A00354:376:HN3JLDSXY:3:2118:10646:19774 99 chr1 3020245 40 4S95M = 3020316 164 TGCTCTTCTTGATGTCCTTTACCATCATCATGAGATATGCTTTTAAATCCAGGTCTACCTTTTCAGGTGTGTTAGGGTGCCCTGGACTGGGCAAAGTGG 68:5=ABGDCFECFAGFDCCBEFECGECGECFEHECBCFHDCCCBC9CGFEHGAGDBEFCBBBFDGF?D?D?@?EDC=BDBA>?)4)<7=47'76-':; NM:i:1 MD:Z:88G6 AS:i:90 XS:i:90 RG:Z:S10192020TN9 MC:Z:3S93M4S MQ:i:40 BI:Z:HHIKGKNNSPMSXKOLOMNNPMMURRSRRSRJRPUWTTJOQNNNQPOQRPUOQOLQSMNNOOOMSOQOOOOONQMQQOOPNRNKPTJNJOPMQQJFHHI BD:Z:JJNK@AKOLQONSOGJOJNIONNOPRPRSPRNLLNROOMPMNIINMHMROPQQJJILNOJNIINOPPJIFIGMONQLKJQROKMPQLILOJOQOHLEGM +A00354:376:HN3JLDSXY:3:2118:10646:19774 147 chr1 3020316 40 3S93M4S = 3020245 -164 TTTGGTGCCCTGGACTGGGCGAAGTGGGTGTTCTGGGTTCTGATGATGGTGAGTGGTCCTGGTTTCTGTTAGTAGGATTCTTACGTTTACCTTTTGACAG 7(';6:==)?<=>8-;<0>97(;4>??>?@=5C@AAA3*EBD4BD@BCBBE)?(@?3.<:')?(B><;',=:=3&<(&<5BCEHBCCCB@;93-6 NM:i:1 MD:Z:16C79 AS:i:91 XS:i:54 RG:Z:S10192020TN9 MC:Z:3S97M MQ:i:60 BI:Z:FHJJJKMKQSPNMOLOOOOORSUQMOQSQQQQONQROKNPMOONOOOMROPLOMOJNORQRUPLQQURLOONOOMOOKRTLRNMTXVNRPQPQMIEHHH BD:Z:LGLLHMHMNONJMGMJJJJJPRSTOJOMILILHNNKFLJONIILFIHNKJOKHKFLHLORQPOOPOQPOJJJJIKINMRMNLHNPSOPQLLJLICHGJJ +A00354:376:HN3JLDSXY:3:2227:20654:21699 99 chr1 3023160 60 5S95M = 3023504 440 TAAGTTGCAAATGAAGCCACAACATAATCAAATTTATGGGACACAATGAAAGCATTCCTAAGAGGAAATTCATAGCTCTGAGTGCCTCCATAATGAAACT 64597@EHECCCFECHHFEEECEECBCCGECCCCCBCFGGEEEEECCFECCHHECCGFDAB>:GFDBAAAEC@?E;0;@:6-;?A(;<>@>='>@A?C@:>C@@)@BC@>DD@BCCDEAA@DABBBCFB@GABBDEBBCEFBDEB@FEBBCEFCDD77686 NM:i:0 MD:Z:70 AS:i:70 XS:i:51 RG:Z:S10192020TN9 MC:Z:5S70M5S MQ:i:60 BI:Z:GINFSWQKOQQTQJPPPKNKOORXRLMNOLONOTOLNMNKNNNNPLMNLSPTQKNNMOQWQKMNPLOOOQROOFEDGHH BD:Z:MJKLPSLMJPOQLMJMJKGMJJPRLMMKPMOHLOONILFLIIINIOMHNPOQLLHMIORQKLLJPMKPMROKKB9JHJJ +A00354:376:HN3JLDSXY:3:2227:20654:21699 147 chr1 3023504 40 96M3S = 3023160 -440 AATCAGAAATGAAAAGGGTGACATTACAACAGATCCTGAAGAAATCCTAAACACCATCAGATCCTTCTACAAAAGGCTATACTCAACAAAACTGGAGTG 88:::<(9:<7:01.<';&-8=0<%:8=',?B>6BDAC@A.)@(B*<&5A>D(*D)C.C/ADFGBD>A@E8BBCEGGABA9@DEB@ABB::ACC;5776 NM:i:2 MD:Z:18A5A71 AS:i:86 XS:i:87 RG:Z:S10192020TN9 MC:Z:5S95M MQ:i:60 BI:Z:KQKDLILOQQLNNNMQMORKNJPPQNKMOJQQWSPNRLNPMORXTQLPNNONNOJWQJPQWSPLTULQNKNNNMMPLSSQNOQKNOLOPOPPTJGHIHH BD:Z:MOIJHNIORQPLLPLPQNQLGOPOLHMMGMJSRQQQPOOJOJPRQQNOJMGIJNMQKLIRQPPNPNNLGMJJOJPRLOOKGKKLMGNKLOJQLG?FJJJ +A00354:376:HN3JLDSXY:3:2208:32570:12399 163 chr1 3024202 60 96M = 3024299 192 CATACCTAAACATGATAAATGCAATATACAGCAAACAACCAGTAGCCAACATCAAAGTAAATGGTGAGAAACTGAAAGAAATCCCAATCAATTCAG 6753;CBAB:DD9EDB7BBBE?DBBABADDGG8BBDD79DD=6@FFDC@C63.(@@.>?44(-C@DACE@>?>=>>B>B?<'88=3;099=6:(798::9<)6-:=-9 NM:i:0 MD:Z:95 AS:i:95 XS:i:0 RG:Z:S10192020TN9 MC:Z:91M5S MQ:i:60 BI:Z:HHKDEILTVRLOOONLPRPNPSLMTRJONNQTPJONKPNNNPSJNNNKQOLPJPQONMQJOQRSQPSQMPQRTNLPTONNPPLPQNLMNLMLILJGLHJN BD:Z:JJII;FJPSQPHKGMNILNINOMNOQNPKJLQONOJJINIINOMFHFJJOOJMPLKMOJMQNMPPOPPOJMPQKOTTNIPPPPUOPQQKNJILOIIMNQP +A00354:376:HN3JLDSXY:3:2641:20473:17440 83 chr1 3027364 60 91M5S = 3027317 -138 GGGTTCTGCTATTATTCTCAAAGCACTTAAGCTTCGTTTTGGTCAGCAGCCTGTGTGCAGTGTGTGGGTGCTGACTGCTTGTTTTGCTTTAAGAGC 99983>;?@:<<;='ADAB?@0;C?FA@ACGGBDADBCCEFEEFDHFDHGHEEEEEHFDEEEEEEFFEEHHEGAHEHHCEECCCEHHCCA@:86:6 NM:i:0 MD:Z:91 AS:i:91 XS:i:0 RG:Z:S10192020TN9 MC:Z:5S95M MQ:i:60 BI:Z:KGGNTNTPLSQQTQUVPRLOORPOOMQQORQMUTNNOOUUNKRKRPKROQNUOTOTOJOPTOUPTQNPTQORLNOTPLTTNOOUVRNQRPIGJKHH BD:Z:LMLNLORSNPOOPOQNLLMJONQJHNNNNMSNPQNNIIPPOKKMNPLMOOOMLMLRPLHLNMNMQOPMSTPNIFPSSNPMNJKRUVQLOKF=JKJJ +A00354:376:HN3JLDSXY:3:1657:25626:30279 65 chr1 3028365 60 4S96M chr3 73001662 0 AAAGTTGAGTTGACATACTTCCGTTAACAAGAATAGTTAGCCAGAAGCCGAACTATAGAAGCTAGAAGCAGGATTAGTAAATACATTTAGAGACTTGTCC 65597@EEHACFEEECBEDCGFBACBCEECHECCBHACBHHFEHECHHFBECE?BCBHEBGGCAGDBFFCFEB@)?D42??'<>><;;.>3=:97685;9 NM:i:0 MD:Z:96 MC:Z:5S91M AS:i:96 XS:i:31 RG:Z:S10192020TN9 BI:Z:HHHFEHKSRPOMRKUSSLNNLPLOMQQMUULUUQSLONPLPMTNVTMQNMTUNOSTTMVUMQRSMVUMQUOQTXRQMORQOQTMUSQNPLUNRGJJEHEI BD:Z:JJGL;DILNJOOMMNQONHNOONHKNOONQONQOPNGLNMSQPPMOMRQOQQOHLOOMMPNSMLMMPNSRPQQRPONHLOJOPONRPJNMLJLJGLJDHM +A00354:376:HN3JLDSXY:3:1119:25482:3818 163 chr1 3029885 60 4S74M5S = 3029885 74 GGTGTATTGCAAAGCAAACAAAACTGTTAGATGAGCACTCACAAGATTCTAGTGTGAATGCTTGGAAGTTGATTTATTAGTGC 69377?ABEGDBBGGDBBDDBBBDCE8BAGDBEDGGDDBEDCC6FCA5DB&E>C>C7@@CE@3BB@2C2=A?<<<;0:9?0<= NM:i:0 MD:Z:74 AS:i:74 XS:i:19 RG:Z:S10192020TN9 MC:Z:5S74M5S MQ:i:60 BI:Z:HHHHELSSMQVUOMQTTNMTTNNMNJNMPLUWJQOPTONPROTTLUWQMQRLNOOORUQJOQNKOSTLOMLQWQNPSQPFHHI BD:Z:JJHG9CKPOSURKOTRPINMPIHMGLGMONNRNLKSRLHLOLMPNLQOOJMNHJGJLQONQNOMPQQOHMMLRQJOQQOKEGN +A00354:376:HN3JLDSXY:3:1119:25482:3818 83 chr1 3029885 60 5S74M5S = 3029885 -74 TGGTGTATTGCAAAGCAAACAAAACTGTTAGATGAGCACTCACAAGATTCTAGTGTGAATGCTTGGAAGTTGATTTATTAGTGC >@@AA>?4B;C@ABFDAB@EBBB@GEECBDGCEGDHFAHEFAFCDGCCEHBDEEEEGCCEHHCEFGCDECEGCCCBCB?:67:6 NM:i:0 MD:Z:74 AS:i:74 XS:i:19 RG:Z:S10192020TN9 MC:Z:4S74M5S MQ:i:60 BI:Z:NGINMTQUUPLOORPLONOLOONOOUNQSQRSSQRPOOORNNKNPQQUULSOOTPSLRSTQLUTOLNNNUSRRPRVRPMEINHH BD:Z:NMJKOPOQSQMJOMPLILFLIILGPMNNLIRRPLMPHFJKIFLNIRNPNNMIMNMPOPQQRMPQONNHNQQTQLQROKD?B@?>A9;><:879;4:8;9 NM:i:0 MD:Z:96 AS:i:96 XS:i:49 RG:Z:S10192020TN9 MC:Z:95M MQ:i:60 BI:Z:HHFHHGMVWPPOUSRMOMPPRQNNNKONRKTRRSTPRSTLPSTMUTMQQONNQPRRNQPRUPOKRXKPNUOVXTQMQONRRNOMSONMLOMMIOJJEJJI BD:Z:JJLE?FLQSLLQOSPNOJLIMNHMGLGJLLNRSPQOROPNPPPNMOMOKPQKMONNJLONPLHLKQMPQPPNRPOOQQROOKOOPQHMNOIMMNOEHGJM +A00354:376:HN3JLDSXY:3:1208:15510:2644 147 chr1 3030486 60 95M5S = 3030334 -247 TTCCTCTAAACTGTGACATCAATCAAGGAACAAGGGCCTCCCCTCCCACTGATGCCAGATAAGGCCCCTTCAGTTCCTTCAGTCTCCTTTGGGGTAGAGC 76<=):799'?<<<=?@=<@>?AACCDADDDEBDDC>EBE@CFEDBEAAABEGFFFGBDECDBDFGBDECDDGDFGBBDEEEC?:86:6 NM:i:0 MD:Z:95 AS:i:95 XS:i:48 RG:Z:S10192020TN9 MC:Z:3S96M MQ:i:60 BI:Z:NMJIQHMLKMMTORKNJWQKQWQKNMOLMOKOMQMNPOSPPQPTQPONNRRSTNOJPQSPNMMNPPPLTQJNMTSPLTQJNJUOSQMOUVSSOLMGJKHH BD:Z:NNNILLNILHROORLHOSMNQRMNOKQOMGMOKORQQLQLLQLQLPJHQPSRRPNLIRONNJQPKKQOQLMIOQPOMOKLHKMKPQOKRSQQPJD&&<====<4@A?B9,C5:>?*CE?@?@@@5EDECEE<>=;>'8;6./::<,<@8>>@@=@@=>@B?AEBD>C4@B6DADDBCCCA9FBACGDGA@EBDFGBDGFECGEBDGDGFEBDE@FGCD92486 NM:i:1 MD:Z:6C89 AS:i:91 XS:i:39 RG:Z:S10192020TN9 MC:Z:3S97M MQ:i:60 BI:Z:JGGGLOORLNIPKNNRQPNNTQJPPNOTMNTULSWQJWUNRLOLRSUOPMPQNOTMTULNTUOULQNJWSPLTTNOJQOJWUNTNPKXRPPRPRGDHFHH BD:Z:JHMLMNQRPPNKMJRQTPKKRLNKMINQPOQNOPRLNRNQPKGMPRQPMKPMHLLNPMNIPMKMMKGNRQQOQSPNKLPMQMPRPPNSMLMSQKF?GMJJ +A00354:376:HN3JLDSXY:3:2342:10963:25833 163 chr1 3032966 60 5S95M = 3033179 303 GCACTTCATCTGAGATCTTCTTCAATTTCTTTCTTCAGAGACTTTAAGTTTTTGTTATACAGACCTTTCCCTTGCTCTGTTAGATTCACACTAAGGTACA 6:76:@EDBFCEDGDB@CBFCBFDBBBBFCBB>CBFDGCFDCBAA@AF5A@@@C>)2@?BB:AAA:2>B@A9AAABAB;>EA@6BCABA@GA)DF7BCEFCEHEHFCCCBDEEGCBCCCCEGAH:EHCEGHCCEGFCCCCEEBCEGFE82:76 NM:i:0 MD:Z:90 AS:i:90 XS:i:83 RG:Z:S10192020TN9 MC:Z:5S95M MQ:i:60 BI:Z:IDHITOPNNOOOUUPUNKROOMQQOOMTTROMTXRKTTXRKXVOUPLOQTRNORQSTQNNUSKNMUUMUSQLOTSOKQQOUUNUYVRPGHHIHH BD:Z:MJFJPOMIOJJJQNMQPLLJHOONNHNOOKGMOQKMOOQKMRNPRPKHNOLHLOROONJJQPKHOQNOPOOMIQPOLONJROQRTSLME?EIJJ +A00354:376:HN3JLDSXY:3:1577:5611:7670 163 chr1 3035865 60 5S94M = 3035912 143 GGAGTAAGGTATTGGCACATCAAAGGAGAAGGATGAGAAGCAGCACAGCAGGTGGCCACCTAAGTGGCGGATGGTCACAGCCAGCCTTGCTAGGCTGGA 69797?AAF@ABBEFGDDD7F9BBGFDGDBGFDBEDGDAFGCFFCCCFECED>-DECBBCA>?:>>7:=?/8><=9;<: NM:i:0 MD:Z:94 AS:i:94 XS:i:55 RG:Z:S10192020TN9 MC:Z:96M4S MQ:i:60 BI:Z:HHMIELPNRPSTRLPNTOTRQRTNLPSOUTLPSWJQOUTLPTNPTOTNQUNPNOPONUPMMRPLNNONSQTWJONKROTNPMTNPMMNKNPPJMJKDIM BD:Z:JJNI:CJOSMNQQMPPRLMQROOHMPQLNQOQQRMKKMPNSRPSRKMPTSQQKJPQRQMPKMOOHJPQOQQRNQKKQNNRUSRRUSMQNRNLMPOKJMN +A00354:376:HN3JLDSXY:3:1577:5611:7670 83 chr1 3035912 60 96M4S = 3035865 -143 TGGCCACCTAAGTGGCGGATGGTCACAGCCAGCCTTGCTAGGCTGGAAGGAGGTAACAACACCATTGGTATTTTTTTTCACACCACTGGCCATCTTAGTG 8:<:94;=79:<=>A;?A>ABA7B>CAEEDBFEGBDGGACEHHEFGCDFGDFEBCAFCAFAGFCCE;EBCCCCCCCCEFAF;GFAHEFHGFCEG@85776 NM:i:0 MD:Z:96 AS:i:96 XS:i:52 RG:Z:S10192020TN9 MC:Z:5S94M MQ:i:60 BI:Z:NGHIJJMIONNOTMUMPRSUNKROOKROPKROQMUUQMSNNQOUPMONPQNNMQMOKMNNNOKQTTNMSPOONOONUQONNNONOOUNPQLZWLKIHIHH BD:Z:NONMGIOLMMHLQRRPPSRQPLLJGMNQPLMPPNPRSMLJQSPPONNKPLJOMMKFLLFIJOMNQQPOPOJJJJIHOJIGIJOIGQRSSRPTNKF@FJJJ +A00354:376:HN3JLDSXY:3:1402:31620:10003 99 chr1 3036042 60 5S95M = 3036101 136 TATGTTGTTTTTTAGGGTGTAGTTTCTGTCTTTTTGTTGGAGTTTTACATTCATTATCCTTTAACGAGATGGATTTGTGGAAAGATATTGTGTAAATTTA 64577@EACCCCCBHGGAFABHACCGDFAGACCCCF+CFGEAACCC(EECCGE78B)?F1BBAB:'D/C)DE8@@@B=B*A>=-><:/077706'66070 NM:i:2 MD:Z:41C17A35 AS:i:85 XS:i:34 RG:Z:S10192020TN9 MC:Z:77M22S MQ:i:60 BI:Z:HHMDEHKPPPPPOQMQPNNNQMNNNMQJOLPNOONKONKOSONMONQMUSRMSSRQTRPNOOQQNNTPVXKPTXROLOOPTUOMVXSSQKNMKNLJJKHJ BD:Z:JJMK:DIGOLLLKPNPKJIFLMFKHNJMGKJOJJJMFLLOPKGLIHMMMQOOPQONOROJNINNNNQKMQMPQRPJMGJPQQJONRPPOLEHEJMGLMGL +A00354:376:HN3JLDSXY:3:1402:31620:10003 147 chr1 3036101 60 77M22S = 3036042 -136 AGAGATGGATTTGTGGAAAGATATTGTGTAAATTTATCTTTGTCATAGAAAATCTTGGTTCTTCTATCTACGGTAAAAGATGAGAACCATCTCCACAGT 9'9;<>>')==>>>>=?6D@@5BB;@?AD@A@ACFA7DCBCFBDGABDGA@AEDABBBCFBDFCFB@FEBDGDEC77676 NM:i:0 MD:Z:77 AS:i:77 XS:i:32 RG:Z:S10192020TN9 MC:Z:5S95M MQ:i:60 BI:Z:JJJKNQMOOMTTOTOLNNPQSSPTTOTLQNRPNPSWULNTUKRKTSPLNORWULTTMMTULTULSWULQNLMLPNNNPQRRPPLNOPKYWQUOIEDHHH BD:Z:GJGPPPOROKRPORQPKPKTPQPQNNNOOJPOJOPRNOJQNLLNPMJOJJPQMMPPONPMNPMMORNNLJPPONHHMIRQOLINMKQOTPNQKA9JFJJ +A00354:376:HN3JLDSXY:3:2436:3748:8578 163 chr1 3036203 60 83M4S = 3036203 83 CTGGGCTAGCATTTGCGTTCTTTTAGGGTGTATATGACATTTGCGGAGGATCTTCTGGCTTTTATAGTCTCTGCTGAGAAGTCACGC 6688=EBAGGDBBBEGA@BFCBBBAGFF@E@ABABEDDCAB6DF@ECFDC@DA@DACDEA@??>>=9?A=?=7<:,760;:? NM:i:0 MD:Z:83 AS:i:83 XS:i:31 RG:Z:S10192020TN9 MC:Z:12S83M4S MQ:i:60 BI:Z:HHDIGIQTNRVSROLORNMLPNNNPLPPNNNQSSSJQJTRQNKORQSOQTWQPOMQKPOQNNNPSSLNLPQPJOQJQOUTLNKLIGN BD:Z:JJJM>HIMPVUSQJMPNILNINHHMMQLKJGLPPOMKKMQOILPNOPKQQRSJOOJMPQNOJJOPPNHKJMJMRNMMMNRPILMJLO +A00354:376:HN3JLDSXY:3:2436:3748:8578 83 chr1 3036203 60 12S83M4S = 3036203 -83 TTACGATCTTCTCTGGGCTAGCATTTGCGTTCTTTTAGGGTGTATATGACATTTGCGGAGGATCTTCTGGCTTTTATAGTCTCTGCTGAGAAGTCACGC 76'5:')=9;-=@2??99&:DB?4(BE@CA9F6BBACEEDEEBCBCEGAFCC9EHBFGDFGCEHCEHEFHHCCCBCBDEEHEHEHHEGDGCDDB<24:6 NM:i:0 MD:Z:83 AS:i:83 XS:i:31 RG:Z:S10192020TN9 MC:Z:83M4S MQ:i:60 BI:Z:JKHGMTRKTUOUNURNQMSRPKQOUUUNNUVMOOQSNRNPUMTTTSSLOKQOUTULOPMOQXVLTVOTMQMNOQSTROJUOUNUQOSRRNQPJLEHLHH BD:Z:LIGLQPLMOMKNQQORTNMNQNOJQSRONPMNIINLJNOLMNOOOQPKFMNHOQQOOLJORQMOQNQQRTOJJNNNKHLMKMPRTRQOLQQIHC=GLJJ +A00354:376:HN3JLDSXY:3:1237:11505:13056 99 chr1 3037494 60 4S96M = 3037569 171 GCGTAGTGGAGAAAAGAAGCATTTTTGAACTCTTGATCTGCTTGCCTACATCTCCTGAGTGCTGAGATTAGAGATTCACACTACTACACTGGTGTGTGTG 6:428E@FGEHECCCHECHHECCCCCFECEDGDCFECGDFHDCFHFDBEECGDGFDFEH@EGCEDGDAA@FCE7@@CAAAA?<>=;==<:<<6:494759 NM:i:0 MD:Z:96 AS:i:96 XS:i:24 RG:Z:S10192020TN9 MC:Z:96M4S MQ:i:60 BI:Z:HHLHHGNPRUQWUOOMUTLPTSQONOLQUNNPQOKQXRPJOQNKPMNSMUSRQQPNKRPOOPRKRPVXRQMVPVXRMSPUPOSMOSLTONJNKKJJHHHH BD:Z:JJLG?EDJRSNPRKJNMPNSSQNHHIMLQOIMJOMLQRILPMNLPPIKNMQSJLOJLKKGIPMLKKMQONMNLNRPOPMNMIMOIMONLHKNIHEGDGDG +A00354:376:HN3JLDSXY:3:1237:11505:13056 147 chr1 3037569 60 96M4S = 3037494 -171 ACTACTACCCTGGTGTGTGTGCTGAAAATTGCACCTAAGGCTTTCTGCCTGCTATGTAAGTACTCTGCACTGAAGCAATATGGGAAGAAACTGATACACG 5=72:71=)?<=<'=;;&(