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polyactis / Accucopy

Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.
https://www.yfish.org/software/Accucopy
GNU General Public License v3.0
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Segmentation Fault #3

Closed sanjitsbatra closed 4 years ago

sanjitsbatra commented 4 years ago

Hi! I am running into a segmentation fault. Why might this be happening?

Here is the infer.status.txt file:

Reading in genome coverage from "/mnt/CT432.bam" ... New chromosome chr1, length=248956422, window size=500, no_of_windows=497913. 59661040 reads so far for "/mnt/CT432.bam". Chromosome chr1 contains 0 valid fragments. New chromosome chr10, length=133797422, window size=500, no_of_windows=267595. 81042310 reads so far for "/mnt/CT432.bam". Chromosome chr10 contains 0 valid fragments. New chromosome chr11, length=135086622, window size=500, no_of_windows=270174. 110417527 reads so far for "/mnt/CT432.bam". Chromosome chr11 contains 0 valid fragments. New chromosome chr12, length=133275309, window size=500, no_of_windows=266551. 139816736 reads so far for "/mnt/CT432.bam". Chromosome chr12 contains 0 valid fragments. New chromosome chr13, length=114364328, window size=500, no_of_windows=228729. 161439829 reads so far for "/mnt/CT432.bam". Chromosome chr13 contains 0 valid fragments. New chromosome chr14, length=107043718, window size=500, no_of_windows=214088. 181255065 reads so far for "/mnt/CT432.bam". Chromosome chr14 contains 0 valid fragments. New chromosome chr15, length=101991189, window size=500, no_of_windows=203983. 199363069 reads so far for "/mnt/CT432.bam". Chromosome chr15 contains 0 valid fragments. New chromosome chr16, length=90338345, window size=500, no_of_windows=180677. 218150818 reads so far for "/mnt/CT432.bam". Chromosome chr16 contains 0 valid fragments. New chromosome chr17, length=83257441, window size=500, no_of_windows=166515. 235637677 reads so far for "/mnt/CT432.bam". Chromosome chr17 contains 0 valid fragments. New chromosome chr18, length=80373285, window size=500, no_of_windows=160747. 253134738 reads so far for "/mnt/CT432.bam". Chromosome chr18 contains 0 valid fragments. New chromosome chr19, length=58617616, window size=500, no_of_windows=117236. 265860905 reads so far for "/mnt/CT432.bam". Chromosome chr19 contains 0 valid fragments. New chromosome chr2, length=242193529, window size=500, no_of_windows=484388. 319870334 reads so far for "/mnt/CT432.bam". Chromosome chr2 contains 0 valid fragments. New chromosome chr20, length=64444167, window size=500, no_of_windows=128889. 333674604 reads so far for "/mnt/CT432.bam". Chromosome chr20 contains 0 valid fragments. New chromosome chr21, length=46709983, window size=500, no_of_windows=93420. 343433771 reads so far for "/mnt/CT432.bam". Chromosome chr21 contains 0 valid fragments. New chromosome chr22, length=50818468, window size=500, no_of_windows=101637. 351723849 reads so far for "/mnt/CT432.bam". Chromosome chr22 contains 0 valid fragments. New chromosome chr3, length=198295559, window size=500, no_of_windows=396592. 396184917 reads so far for "/mnt/CT432.bam". Chromosome chr3 contains 0 valid fragments. New chromosome chr4, length=190214555, window size=500, no_of_windows=380430. 441143709 reads so far for "/mnt/CT432.bam". Chromosome chr4 contains 0 valid fragments. New chromosome chr5, length=181538259, window size=500, no_of_windows=363077. 482509996 reads so far for "/mnt/CT432.bam". Chromosome chr5 contains 0 valid fragments. New chromosome chr6, length=170805979, window size=500, no_of_windows=341612. 518332470 reads so far for "/mnt/CT432.bam". Chromosome chr6 contains 0 valid fragments. New chromosome chr7, length=159345973, window size=500, no_of_windows=318692. 562631614 reads so far for "/mnt/CT432.bam". Chromosome chr7 contains 0 valid fragments. New chromosome chr8, length=145138636, window size=500, no_of_windows=290278. 594804392 reads so far for "/mnt/CT432.bam". Chromosome chr8 contains 0 valid fragments. New chromosome chr9, length=138394717, window size=500, no_of_windows=276790. 653668784 reads so far for "/mnt/CT432.bam". Chromosome chr9 contains 0 valid fragments. Reading and smoothing of coverage from "/mnt/CT432.bam" is Done. 22 unique chromosomes, 653668784 reads. Genome wide mean coverage is 0 Reading in genome coverage from "/mnt/CT434.bam" ... New chromosome chr1, length=248956422, window size=500, no_of_windows=497913. 21543443 reads so far for "/mnt/CT434.bam". Chromosome chr1 contains 0 valid fragments. New chromosome chr10, length=133797422, window size=500, no_of_windows=267595. 33519753 reads so far for "/mnt/CT434.bam". Chromosome chr10 contains 0 valid fragments. New chromosome chr11, length=135086622, window size=500, no_of_windows=270174. 45224913 reads so far for "/mnt/CT434.bam". Chromosome chr11 contains 0 valid fragments. New chromosome chr12, length=133275309, window size=500, no_of_windows=266551. 57193479 reads so far for "/mnt/CT434.bam". Chromosome chr12 contains 0 valid fragments. New chromosome chr13, length=114364328, window size=500, no_of_windows=228729. 65967040 reads so far for "/mnt/CT434.bam". Chromosome chr13 contains 0 valid fragments. New chromosome chr14, length=107043718, window size=500, no_of_windows=214088. 73940039 reads so far for "/mnt/CT434.bam". Chromosome chr14 contains 0 valid fragments. New chromosome chr15, length=101991189, window size=500, no_of_windows=203983. 81214655 reads so far for "/mnt/CT434.bam". Chromosome chr15 contains 0 valid fragments. New chromosome chr16, length=90338345, window size=500, no_of_windows=180677. 88145461 reads so far for "/mnt/CT434.bam". Chromosome chr16 contains 0 valid fragments. New chromosome chr17, length=83257441, window size=500, no_of_windows=166515. 95287511 reads so far for "/mnt/CT434.bam". Chromosome chr17 contains 0 valid fragments. New chromosome chr18, length=80373285, window size=500, no_of_windows=160747. 102166467 reads so far for "/mnt/CT434.bam". Chromosome chr18 contains 0 valid fragments. New chromosome chr19, length=58617616, window size=500, no_of_windows=117236. 106899655 reads so far for "/mnt/CT434.bam". Chromosome chr19 contains 0 valid fragments. New chromosome chr2, length=242193529, window size=500, no_of_windows=484388. 128578844 reads so far for "/mnt/CT434.bam". Chromosome chr2 contains 0 valid fragments. New chromosome chr20, length=64444167, window size=500, no_of_windows=128889. 133963433 reads so far for "/mnt/CT434.bam". Chromosome chr20 contains 0 valid fragments. New chromosome chr21, length=46709983, window size=500, no_of_windows=93420. 137937298 reads so far for "/mnt/CT434.bam". Chromosome chr21 contains 0 valid fragments. New chromosome chr22, length=50818468, window size=500, no_of_windows=101637. 141126722 reads so far for "/mnt/CT434.bam". Chromosome chr22 contains 0 valid fragments. New chromosome chr3, length=198295559, window size=500, no_of_windows=396592. 159234832 reads so far for "/mnt/CT434.bam". Chromosome chr3 contains 0 valid fragments. New chromosome chr4, length=190214555, window size=500, no_of_windows=380430. 177053732 reads so far for "/mnt/CT434.bam". Chromosome chr4 contains 0 valid fragments. New chromosome chr5, length=181538259, window size=500, no_of_windows=363077. 193446228 reads so far for "/mnt/CT434.bam". Chromosome chr5 contains 0 valid fragments. New chromosome chr6, length=170805979, window size=500, no_of_windows=341612. 209476810 reads so far for "/mnt/CT434.bam". Chromosome chr6 contains 0 valid fragments. New chromosome chr7, length=159345973, window size=500, no_of_windows=318692. 223320566 reads so far for "/mnt/CT434.bam". Chromosome chr7 contains 0 valid fragments. New chromosome chr8, length=145138636, window size=500, no_of_windows=290278. 236709378 reads so far for "/mnt/CT434.bam". Chromosome chr8 contains 0 valid fragments. New chromosome chr9, length=138394717, window size=500, no_of_windows=276790. 263020395 reads so far for "/mnt/CT434.bam". Chromosome chr9 contains 0 valid fragments. Reading and smoothing of coverage from "/mnt/CT434.bam" is Done. 22 unique chromosomes, 263020395 reads. Genome wide mean coverage is 0 Outputting normalized coverage ratio of chr1 ... Output done. Outputting normalized coverage ratio of chr2 ... Output done. Outputting normalized coverage ratio of chr3 ... Output done. Outputting normalized coverage ratio of chr4 ... Output done. Outputting normalized coverage ratio of chr5 ... Output done. Outputting normalized coverage ratio of chr6 ... Output done. Outputting normalized coverage ratio of chr7 ... Output done. Outputting normalized coverage ratio of chr8 ... Output done. Outputting normalized coverage ratio of chr9 ... Output done. Outputting normalized coverage ratio of chr10 ... Output done. Outputting normalized coverage ratio of chr11 ... Output done. Outputting normalized coverage ratio of chr12 ... Output done. Outputting normalized coverage ratio of chr13 ... Output done. Outputting normalized coverage ratio of chr14 ... Output done. Outputting normalized coverage ratio of chr15 ... Output done. Outputting normalized coverage ratio of chr16 ... Output done. Outputting normalized coverage ratio of chr17 ... Output done. Outputting normalized coverage ratio of chr18 ... Output done. Outputting normalized coverage ratio of chr19 ... Output done. Outputting normalized coverage ratio of chr20 ... Output done. Outputting normalized coverage ratio of chr21 ... Output done. Outputting normalized coverage ratio of chr22 ... Output done. program name is /usr/local/Accucopy/GADA. Reading data from /mnt/output_CT432_CT434/chr14.ratio.w500.csv.gz ... program name is /usr/local/Accucopy/GADA. Reading data from /mnt/output_CT432_CT434/chr22.ratio.w500.csv.gz ... 0 data points for chromosome chr14. Running SBLandBE ... 0 data points for chromosome chr22. Running SBLandBE ...

polyactis commented 4 years ago

It seems strange your bam file contains reads but the coverage from it is zero. Can you send us a small piece of your bam file (first 5000 lines) for examination?

Maybe the chromosome IDs do not match that of the reference genome file. The reference genome file we provided uses "chr1", not "1". Best,

Yu Huang Professor, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, CAS http://www.yfish.org/ https://sites.google.com/site/polyactis/

On Sat, Oct 10, 2020 at 11:43 AM Sanjit Singh Batra < notifications@github.com> wrote:

Hi! I am running into a segmentation fault. Why might this be happening?

Here is the infer.status.txt file:

Reading in genome coverage from "/mnt/CT432.bam" ... New chromosome chr1, length=248956422, window size=500, no_of_windows=497913. 59661040 reads so far for "/mnt/CT432.bam". Chromosome chr1 contains 0 valid fragments. New chromosome chr10, length=133797422, window size=500, no_of_windows=267595. 81042310 reads so far for "/mnt/CT432.bam". Chromosome chr10 contains 0 valid fragments. New chromosome chr11, length=135086622, window size=500, no_of_windows=270174. 110417527 reads so far for "/mnt/CT432.bam". Chromosome chr11 contains 0 valid fragments. New chromosome chr12, length=133275309, window size=500, no_of_windows=266551. 139816736 reads so far for "/mnt/CT432.bam". Chromosome chr12 contains 0 valid fragments. New chromosome chr13, length=114364328, window size=500, no_of_windows=228729. 161439829 reads so far for "/mnt/CT432.bam". Chromosome chr13 contains 0 valid fragments. New chromosome chr14, length=107043718, window size=500, no_of_windows=214088. 181255065 reads so far for "/mnt/CT432.bam". Chromosome chr14 contains 0 valid fragments. New chromosome chr15, length=101991189, window size=500, no_of_windows=203983. 199363069 reads so far for "/mnt/CT432.bam". Chromosome chr15 contains 0 valid fragments. New chromosome chr16, length=90338345, window size=500, no_of_windows=180677. 218150818 reads so far for "/mnt/CT432.bam". Chromosome chr16 contains 0 valid fragments. New chromosome chr17, length=83257441, window size=500, no_of_windows=166515. 235637677 reads so far for "/mnt/CT432.bam". Chromosome chr17 contains 0 valid fragments. New chromosome chr18, length=80373285, window size=500, no_of_windows=160747. 253134738 reads so far for "/mnt/CT432.bam". Chromosome chr18 contains 0 valid fragments. New chromosome chr19, length=58617616, window size=500, no_of_windows=117236. 265860905 reads so far for "/mnt/CT432.bam". Chromosome chr19 contains 0 valid fragments. New chromosome chr2, length=242193529, window size=500, no_of_windows=484388. 319870334 reads so far for "/mnt/CT432.bam". Chromosome chr2 contains 0 valid fragments. New chromosome chr20, length=64444167, window size=500, no_of_windows=128889. 333674604 reads so far for "/mnt/CT432.bam". Chromosome chr20 contains 0 valid fragments. New chromosome chr21, length=46709983, window size=500, no_of_windows=93420. 343433771 reads so far for "/mnt/CT432.bam". Chromosome chr21 contains 0 valid fragments. New chromosome chr22, length=50818468, window size=500, no_of_windows=101637. 351723849 reads so far for "/mnt/CT432.bam". Chromosome chr22 contains 0 valid fragments. New chromosome chr3, length=198295559, window size=500, no_of_windows=396592. 396184917 reads so far for "/mnt/CT432.bam". Chromosome chr3 contains 0 valid fragments. New chromosome chr4, length=190214555, window size=500, no_of_windows=380430. 441143709 reads so far for "/mnt/CT432.bam". Chromosome chr4 contains 0 valid fragments. New chromosome chr5, length=181538259, window size=500, no_of_windows=363077. 482509996 reads so far for "/mnt/CT432.bam". Chromosome chr5 contains 0 valid fragments. New chromosome chr6, length=170805979, window size=500, no_of_windows=341612. 518332470 reads so far for "/mnt/CT432.bam". Chromosome chr6 contains 0 valid fragments. New chromosome chr7, length=159345973, window size=500, no_of_windows=318692. 562631614 reads so far for "/mnt/CT432.bam". Chromosome chr7 contains 0 valid fragments. New chromosome chr8, length=145138636, window size=500, no_of_windows=290278. 594804392 reads so far for "/mnt/CT432.bam". Chromosome chr8 contains 0 valid fragments. New chromosome chr9, length=138394717, window size=500, no_of_windows=276790. 653668784 reads so far for "/mnt/CT432.bam". Chromosome chr9 contains 0 valid fragments. Reading and smoothing of coverage from "/mnt/CT432.bam" is Done. 22 unique chromosomes, 653668784 reads. Genome wide mean coverage is 0 Reading in genome coverage from "/mnt/CT434.bam" ... New chromosome chr1, length=248956422, window size=500, no_of_windows=497913. 21543443 reads so far for "/mnt/CT434.bam". Chromosome chr1 contains 0 valid fragments. New chromosome chr10, length=133797422, window size=500, no_of_windows=267595. 33519753 reads so far for "/mnt/CT434.bam". Chromosome chr10 contains 0 valid fragments. New chromosome chr11, length=135086622, window size=500, no_of_windows=270174. 45224913 reads so far for "/mnt/CT434.bam". Chromosome chr11 contains 0 valid fragments. New chromosome chr12, length=133275309, window size=500, no_of_windows=266551. 57193479 reads so far for "/mnt/CT434.bam". Chromosome chr12 contains 0 valid fragments. New chromosome chr13, length=114364328, window size=500, no_of_windows=228729. 65967040 reads so far for "/mnt/CT434.bam". Chromosome chr13 contains 0 valid fragments. New chromosome chr14, length=107043718, window size=500, no_of_windows=214088. 73940039 reads so far for "/mnt/CT434.bam". Chromosome chr14 contains 0 valid fragments. New chromosome chr15, length=101991189, window size=500, no_of_windows=203983. 81214655 reads so far for "/mnt/CT434.bam". Chromosome chr15 contains 0 valid fragments. New chromosome chr16, length=90338345, window size=500, no_of_windows=180677. 88145461 reads so far for "/mnt/CT434.bam". Chromosome chr16 contains 0 valid fragments. New chromosome chr17, length=83257441, window size=500, no_of_windows=166515. 95287511 reads so far for "/mnt/CT434.bam". Chromosome chr17 contains 0 valid fragments. New chromosome chr18, length=80373285, window size=500, no_of_windows=160747. 102166467 reads so far for "/mnt/CT434.bam". Chromosome chr18 contains 0 valid fragments. New chromosome chr19, length=58617616, window size=500, no_of_windows=117236. 106899655 reads so far for "/mnt/CT434.bam". Chromosome chr19 contains 0 valid fragments. New chromosome chr2, length=242193529, window size=500, no_of_windows=484388. 128578844 reads so far for "/mnt/CT434.bam". Chromosome chr2 contains 0 valid fragments. New chromosome chr20, length=64444167, window size=500, no_of_windows=128889. 133963433 reads so far for "/mnt/CT434.bam". Chromosome chr20 contains 0 valid fragments. New chromosome chr21, length=46709983, window size=500, no_of_windows=93420. 137937298 reads so far for "/mnt/CT434.bam". Chromosome chr21 contains 0 valid fragments. New chromosome chr22, length=50818468, window size=500, no_of_windows=101637. 141126722 reads so far for "/mnt/CT434.bam". Chromosome chr22 contains 0 valid fragments. New chromosome chr3, length=198295559, window size=500, no_of_windows=396592. 159234832 reads so far for "/mnt/CT434.bam". Chromosome chr3 contains 0 valid fragments. New chromosome chr4, length=190214555, window size=500, no_of_windows=380430. 177053732 reads so far for "/mnt/CT434.bam". Chromosome chr4 contains 0 valid fragments. New chromosome chr5, length=181538259, window size=500, no_of_windows=363077. 193446228 reads so far for "/mnt/CT434.bam". Chromosome chr5 contains 0 valid fragments. New chromosome chr6, length=170805979, window size=500, no_of_windows=341612. 209476810 reads so far for "/mnt/CT434.bam". Chromosome chr6 contains 0 valid fragments. New chromosome chr7, length=159345973, window size=500, no_of_windows=318692. 223320566 reads so far for "/mnt/CT434.bam". Chromosome chr7 contains 0 valid fragments. New chromosome chr8, length=145138636, window size=500, no_of_windows=290278. 236709378 reads so far for "/mnt/CT434.bam". Chromosome chr8 contains 0 valid fragments. New chromosome chr9, length=138394717, window size=500, no_of_windows=276790. 263020395 reads so far for "/mnt/CT434.bam". Chromosome chr9 contains 0 valid fragments. Reading and smoothing of coverage from "/mnt/CT434.bam" is Done. 22 unique chromosomes, 263020395 reads. Genome wide mean coverage is 0 Outputting normalized coverage ratio of chr1 ... Output done. Outputting normalized coverage ratio of chr2 ... Output done. Outputting normalized coverage ratio of chr3 ... Output done. Outputting normalized coverage ratio of chr4 ... Output done. Outputting normalized coverage ratio of chr5 ... Output done. Outputting normalized coverage ratio of chr6 ... Output done. Outputting normalized coverage ratio of chr7 ... Output done. Outputting normalized coverage ratio of chr8 ... Output done. Outputting normalized coverage ratio of chr9 ... Output done. Outputting normalized coverage ratio of chr10 ... Output done. Outputting normalized coverage ratio of chr11 ... Output done. Outputting normalized coverage ratio of chr12 ... Output done. Outputting normalized coverage ratio of chr13 ... Output done. Outputting normalized coverage ratio of chr14 ... Output done. Outputting normalized coverage ratio of chr15 ... Output done. Outputting normalized coverage ratio of chr16 ... Output done. Outputting normalized coverage ratio of chr17 ... Output done. Outputting normalized coverage ratio of chr18 ... Output done. Outputting normalized coverage ratio of chr19 ... Output done. Outputting normalized coverage ratio of chr20 ... Output done. Outputting normalized coverage ratio of chr21 ... Output done. Outputting normalized coverage ratio of chr22 ... Output done. program name is /usr/local/Accucopy/GADA. Reading data from /mnt/output_CT432_CT434/chr14.ratio.w500.csv.gz ... program name is /usr/local/Accucopy/GADA. Reading data from /mnt/output_CT432_CT434/chr22.ratio.w500.csv.gz ... 0 data points for chromosome chr14. Running SBLandBE ... 0 data points for chromosome chr22. Running SBLandBE ...

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sanjitsbatra commented 4 years ago

Yes, that the coverage is 0 is indeed surprising. Here is a sample of lines from the bam file:

E00435:54:H3LH5CCXY:6:1212:13210:39528 145 chr1 9996 19 115S36M chr16 25760102 0 AAACCATCACCCTGACCCACACCCTAACTCTAATCAGAGCCCTAACCCTATCCCCAACCCTTACCCATACCCCGACCCCAACCCAGACCCACACCCTTACCCTACCCCTAGCCCTTCCGATAACCCTAACCCTAACCCTAACCCTAACCCT 7-A---)))-7)7))7)7))-7-7--7-------7)---A--<7-<--A7-A-7--F<-------7----7----A7---7JF7--<AA7-AFF-F7-7AJFF77-7-A-7A-7<7-<--<---A7<<<JFJJJJJFFJFAFJ<FF<FA<A NM:i:0 MD:Z:36 MC:Z:46M105S AS:i:36 XS:i:32 SA:Z:chr7,16583804,+,41S22M88S,18,0;chr1,99836632,+,90S19M42S,0,0;chrX,70282341,+,56S19M76S,0,0; XA:Z:chr6,-147869,119S32M,0;chr22,+50808438,32M119S,0; E00435:54:H3LH5CCXY:8:2215:21227:67058 113 chr1 9998 34 40S111M chr22 50808375 0 GTCAACATAATCCTAACACTACCTCTCACATTAGCACTAACGATAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC ----77-<7--77<----7--7--77--7-----A<JA-777-FA-FJAF<JF<FFA7-A-J<FFJFJAJF-AJFAF77-F-FJFJJJJJF<-A<JJFA-JJJJJJJFJJ<JJJJJJJJJJJJJFJJJJJJJJJJJJFJJJJJJJJFFFAA NM:i:2 MD:Z:31C27A51 MC:Z:60S91M AS:i:101 XS:i:86 XA:Z:chr22,+50808362,12M1I96M42S,4;chr12,-10224,43S90M7D18M,9; E00435:54:H3LH5CCXY:5:2119:6796:7849 65 chr1 9999 0 9M1D101M41S chrY 57216993 0 GATCACCCTACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFFFJJFJJFJJ<JJJJJFJJJJJFJJJJJ<AJFFJJ<FFJJJ7FAFJAAJFFFJJJ7FJJ7A--7A<AAA-7<)-F- NM:i:3 MD:Z:3A5^A6A94 MC:Z:100M51S AS:i:96 XS:i:95 E00435:54:H3LH5CCXY:6:2107:32045:43114 161 chr1 9999 0 3M1I108M39S chr10 10039 0 GATCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTC AAFFFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJAJFJJJJJJAFFJAFJJFAA7AAFA<-7A<F<FJAJ<AJJJ<FAFF777FF7-7--7 NM:i:1 MD:Z:111 MC:Z:44S107M AS:i:108 XS:i:107 E00435:54:H3LH5CCXY:6:2207:2229:44521 161 chr1 9999 0 3M1I108M39S chr5 10638 0 GATCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJFJJJJJFFJJJJJJFJJJJJFFJJJFJAAF<FJ<J-FJ)AJ7<AFJJJ-<A<-<---7-AFF-7 NM:i:1 MD:Z:111 MC:Z:44S107M AS:i:108 XS:i:107 E00435:54:H3LH5CCXY:8:1123:9496:48916 2113 chr1 9999 0 62H60M29H chr5 18606783 0 GATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJ NM:i:0 MD:Z:60 MC:Z:44M107H AS:i:60 XS:i:59 SA:Z:chr5,18606834,-,80S71M,60,0;chr5,18606796,-,31M120S,60,0; XA:Z:chr22,-50808411,29S59M63S,0;chr7,+10026,64S59M28S,0;chr1,+180749,67S56M28S,0;chr1,+180788,64S14M2D45M28S,2; E00435:54:H3LH5CCXY:8:1123:9496:48916 2225 chr1 9999 0 49H60M42H chr5 18606834 0 GATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC JJJJJJJJJJJJJFFFJJJJJJFJJJFJFJJJJ<JJJJJFJJJJJJFJJJJFJJJJJJJJ NM:i:0 MD:Z:60 MC:Z:80H71M AS:i:60 XS:i:59 SA:Z:chr5,18606783,+,44M107S,60,0;chr5,18606834,+,93S58M,60,0; XA:Z:chr7,-10026,51S59M41S,0;chr22,+50808411,42S59M50S,0;chr1,-180749,54S56M41S,0; E00435:54:H3LH5CCXY:8:1103:9516:27011 2209 chr1 10000 0 12H106M33H = 10000 105 ATAACCCTAACCCTAACCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ7J7FFJAA-FFJAAFF7AAA<AAJ7A- NM:i:1 MD:Z:18C87 MC:Z:46H105M AS:i:101 XS:i:100 SA:Z:chrX,6865189,-,131S20M,6,0; E00435:54:H3LH5CCXY:8:2215:13169:3594 161 chr1 10000 24 106M1I44M chr5 11581 0 CTAACCCTAACCCTAACCCTAACCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC AAFFFJJJJJJJJJJJJJJJJJJJ<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJJFFJJJFJFJJFF--7FFA-7<FF-)-)A<7A-<<7A7-AFFFJJJJ<----<<F----A<7-AFFF NM:i:3 MD:Z:0A23C125 MC:Z:2S149M AS:i:137 XS:i:125 E00435:54:H3LH5CCXY:5:2210:31456:67902 177 chr1 10000 0 103S48M chrX 156030350 0 CCAAACCCCACACCTACCCCTACCCATCACAATAACACAACCCCCAACCCACACCCAACCCCCAACCCAAACCCTACCCCCTACCCGAACCCAACCCCCAACCATAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACC 7--77-<<)77-7))7)-7)-7------AA7-7----7)))--77A7-7----7--7777-7-77<----7-JAFA777----77--7-FA7---7---<7-<-F<-7-7-F-JJJJF-JFF-<FJF7-<AFJFF77-JF-FAFFAFFFAA NM:i:1 MD:Z:25T22 MC:Z:151M AS:i:43 XS:i:43 SA:Z:chr4,37544732,+,77S20M54S,0,0; E00435:54:H3LH5CCXY:6:2101:12794:24321 113 chr1 10000 0 66S85M chr12 133264930 0 CTACCCCTAACCATCCCAATAACCCTCACCATAAACCTAACCATAAACCTAACACTAACCATAACCATAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC )7)A77-777A7-7---7-AA7))7--77FFJJA7--AJFA7777777<7-7--AF<77<--F7-<<-FA7AAAF7A-7A-FJA<FJJ<FFJ-AJJFJJF<-F7A7FJJJJJJJFF<--<-FJ7AF-FFFFF7JJJJJJJJAJJJFFFAA< NM:i:1 MD:Z:35C49 MC:Z:15S136M AS:i:80 XS:i:80 SA:Z:chrY,9108041,+,84S32M35S,25,1;chr15,78045364,-,15S22M114S,18,0; E00435:54:H3LH5CCXY:8:1103:9516:27011 113 chr1 10000 0 46S105M chrX 6865189 0 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCCCTAACTATAATAACCCTAACCCTAACCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA AFJJJJJJJJJJJJJJJJJJJJJJAJFJJJJJJJJJJJJJJJ<JFJF<JFFAJJAJJJJJJJJJJJFJFFJJJJJAJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJFFFFAA NM:i:1 MD:Z:18C86 MC:Z:131S20M AS:i:100 XS:i:99 SA:Z:chrX,6865189,+,97S20M34S,6,0; E00435:54:H3LH5CCXY:8:1221:26291:12472 81 chr1 10000 0 44S98M1D9M chr12 10202 0 TCCCTACCCATAATCTTCACCTAACCCTTATCCCTACCCTTACTATAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACC --)7---7-----------------FA--77-7--F7--7-77--AJF7-7-F7----JAAA77-<--A7-A-------A-A<--F7-7<JA<<--JAA<JA7F-7<-7JFF--AJJF7-F<FJF<<FAF--FFAJJAJJFJAFJFFA<AA NM:i:2 MD:Z:7T90^A9 MC:Z:85M66S AS:i:95 XS:i:94 SA:Z:chr16,7641599,-,27S19M105S,0,0; E00435:54:H3LH5CCXY:8:2102:4188:70240 177 chr1 10000 0 44S107M chr12 133263387 0 ACACACACCTCACCCTATTGCTAACTACATTCCTATCTCTTCCCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC -7-)-)-)-7)77---------<-7-------------)---7--7--AF<<7-FA-7--FF7FJ<FJJJJJJJAAJ7JJJFJFFJFFFFFJJFJAJJJFJFJJJFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFJJFFFAA NM:i:0 MD:Z:107 MC:Z:71S80M AS:i:107 XS:i:106 SA:Z:chr3,194033747,-,25S21M105S,9,0; E00435:54:H3LH5CCXY:7:2204:8359:42411 65 chr1 10001 0 110M41S chrX 156030509 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCGAACCCTAACCCCAACCCTAACCCAAACCCAGATCGGAATAGCACACGGCTGAACTCCAGTCTCGCG AAFAF<FJJA<FAAF-FFAF<7<7<JJ<-<<7AAFA-7-<A<7JA-<F7FJ<--A7<JA<FFAJ77FAJFJ7---AFAJF--<7--77-7--<--7-7-A7FJ7J-<-FA-7------7-7------A-7-7)-))-F--7-<JJ)--A7) NM:i:2 MD:Z:84T11T13 MC:Z:114M37S AS:i:100 XS:i:99 E00435:54:H3LH5CCXY:7:2207:7923:42851 161 chr1 10001 0 109M42S chr5 9999 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGCAGAGCGTCGTGTAGGGACAGAGTGTAGATCCCGGG AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<FJJFFJAFJJ7<-FJF--FAFA-)7-)77))AA-)-<-F<-)7AAJ77<<-FAF-)7-) NM:i:0 MD:Z:109 MC:Z:41S110M AS:i:109 XS:i:108 E00435:54:H3LH5CCXY:8:1102:26220:7884 65 chr1 10001 7 4S30M1I75M1I40M chrX 156030473 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJFFFJJFAJAJJJFFJJJJF<JJJJFA<AJJAFFJJJ--FAJJF-FAFF--AFJJAA7A7A-<JJJJ7-7FJJ7- NM:i:2 MD:Z:145 MC:Z:147M4S AS:i:131 XS:i:126 E00435:54:H3LH5CCXY:8:2105:13464:5792 161 chr1 10001 0 102M1I29M19S chr5 10953 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCAAACCCAAAACCCAACCCTAACCCTAACCCTAACCCCCCCTCCAACCCCAACCCC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJ7J-A7FFJJFAJJJJA-FJFJAJF---7---<AF-F-7-7-7-----7-AJ--7-7-)7A---------<AF---A<<))))))))--)7)7))7)) NM:i:4 MD:Z:90T5T5T28 MC:Z:151M AS:i:109 XS:i:108 SA:Z:chr9,38301718,-,20M131S,6,0; E00435:54:H3LH5CCXY:6:1203:7862:60853 113 chr1 10001 17 57M1I6M1I86M chr22 50808383 0 TACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACGCTAACCCTAACCC --)FA7-7-JF7--AFJAA7-J<7---FAA-7-JFA7-7FF7---FFJA-7FJFA--JAFF-FJJJJJAFJJJJJ<AJJJJFFJJJFF-JJJFJ<JJJJF-JJJJFFJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA NM:i:4 MD:Z:2A132C13 MC:Z:53S82M16S AS:i:127 XS:i:118 E00435:54:H3LH5CCXY:6:2209:21562:41022 113 chr1 10001 0 12S55M2I82M chr12 133264931 0 GATCCCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCC AA)JJJJJJJJJJAJJJJJJ7JJFJJJJJFJJJJJJFJFJJJFAFJJFJFAJJJJJJJJJJJAJJFJJJAAJJFJFFJJJFJAJJJJJFJJJJJFJJJJJFJJJJJAJJJJJ<JJJJJ<JJJJFJJJJJJJJJJJJJJJJJJJJJJFFFAA NM:i:2 MD:Z:137 MC:Z:29M1D52M4D62M8S AS:i:129 XS:i:128 XA:Z:chr5,-11521,8S59M1I54M1D29M,2;chr5,-11425,8S61M4D53M1D29M,5;chr4,+190122865,29M2D43M3D8M2I65M4S,7;chr7,-10004,8S61M19D52M4D30M,24;chr4,+190122800,80M2I14M1D47M8S,7; E00435:54:H3LH5CCXY:6:2213:18385:54928 113 chr1 10001 17 60M2I89M chrX 156030584 0 TAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCCACCCCCTCACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACGCTAACCCTAACCC --)A)<)<7F<7--<J<F---A<7-7-A-7---JFA-7A<77---AA7-7-A77-7--7JA--FFJJJJJJJJJJ<FJJJFFJJJJJF-JJJJJAJJJJJJJJJJJFJJJFJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJFAFAA NM:i:9 MD:Z:6T35T11T1A3T1A72C13 MC:Z:23S21M5I86M16S AS:i:106 XS:i:96 E00435:54:H3LH5CCXY:8:2219:24830:54453 113 chr1 10001 0 57M2I92M chrY 57217095 0 TACCCCCAACCCCAACCCTAACCCTAACCCTCACCCCAACCCTAACCCTAACCCTAACCCCCAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACGCTAACCCTAACCC ))--77))7A-7)-7FF7---AA7---FF7--<F77--77A7--7F-A7--7<<---A7A7--JJJJJJJ<JJJJJJJJJJJFJJJJJAJJJJJFJJJJJFJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA NM:i:10 MD:Z:2A3T5T18A4T23T1A72C13 MC:Z:2S45M1D88M16S AS:i:104 XS:i:102 E00435:54:H3LH5CCXY:7:2206:2534:58761 129 chr1 10002 0 109M42S chr13 114354220 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCAAACCGGAACAGCGACGGACAGGGAAAGAGTGAACATCTCGGTC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJAFJJJJFJJJFJJJJJJJFJJJFJ-AAFF-7-F---)7))-7F)-A))))7))))A-7---------<-<-))) NM:i:1 MD:Z:101T7 MC:Z:110M41S AS:i:104 XS:i:102 E00435:54:H3LH5CCXY:8:1214:27428:11839 65 chr1 10002 0 77M1D14M1I59M chrY 57217010 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCCTAACCCAACCCCAACCCCAACCCTAACACTAACCCTAACCCCAACCCTAACCCCCA AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJ-F-AF7-A-AF7-F7FJ--A-AJ--A--A--A-7F--7-AF-7---7-77<FJ-7<-<A--A)J<-7-<JA)7) NM:i:8 MD:Z:77^T23T1A8T9C13T12T1 MC:Z:151M AS:i:109 XS:i:109 E00435:54:H3LH5CCXY:7:2105:12784:53557 177 chr1 10002 11 7S104M1I39M chrY 57217049 0 CACCCCCAACCCCAACCCTCACCCTAACCCTAACCCTAACCCCAACCCTACCCCTAACCCTAACCCTACCCCTCCCCCTAACCCCACCCCTACCCCTCACCCCACCCCTAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT )-)7-7))))-7)A7)<-))-------<<----<<--))7A)---AF7---A7-7--7--A-F7-7-7--77---<---7-A---F-<F-A7FJA7--7A77---AF-<--A77-<AJJJJJJJJJJJFJJJJJFJJJJJJJJJJJFFFAA NM:i:14 MD:Z:5T6A22T7A17A4A0A9T1A5A4A4T1A45 MC:Z:5S146M AS:i:71 XS:i:63 XA:Z:chr4,+190122752,36M1I16M1I90M7S,15;chr3,-10541,7S25M5D72M1I46M,20; E00435:54:H3LH5CCXY:5:2210:3062:9079 129 chr1 10003 0 108M43S chr4 190122959 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCGTAACAGCAACGCTAACGCTAAGAGTGCAGATACCACTCA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJFJFJJJJJFJJJFJFJJJ77-FJFAFFJJJ-A7FA--7-AAFA7FFFA7--F-----<---7--A)7--<-----------)-)-7<-<---)- NM:i:0 MD:Z:108 MC:Z:48M1I58M44S AS:i:108 XS:i:106 SA:Z:chr17,54587560,-,19M132S,0,0; E00435:54:H3LH5CCXY:6:2122:15828:35590 129 chr1 10003 0 107M44S chr18 80262963 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTGTAGGAAAGAGTGTAGATCTCTGTGGC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFJJFJJJJAF<-A<)-7)--7<)<7))AFFA7--<-A-<F-<7<FFJ--7<)) NM:i:0 MD:Z:107 MC:Z:106M45S AS:i:107 XS:i:106 E00435:54:H3LH5CCXY:6:2122:15473:50305 161 chr1 10003 0 107M44S chr10 10094 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGCGCGTCGCGTAGGAAAGAGTGTAGATCTCGGTGGT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJF7FJFJAAJFJJFJJFFJ7<JA<<A7-AAJJ<AJFJF<<AJJAFFFFFFJJJJFJJFJJAAAFJFF<)<-AAJFFA)-A-)7<)-<)<AA--7A--A<-<7FA<FAJ7)-- NM:i:0 MD:Z:107 MC:Z:45S106M AS:i:107 XS:i:106 E00435:54:H3LH5CCXY:7:1210:26118:51060 97 chr1 10003 0 107M44S chr5 11666 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJFJJJJJFFJJJJJFJJJJFJAJJ<-FJAAFFJ<AAFJJ-FAF<JJFJFFFJFAF<FFF-AF- NM:i:0 MD:Z:107 MC:Z:45S106M AS:i:107 XS:i:106 E00435:54:H3LH5CCXY:7:1210:25479:51254 97 chr1 10003 0 107M44S chr5 10273 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJFJAJJJJFJFJJJJJFJJJFJJJFJJFF<FAAJJ7<<A<FFFFFFAJFFAJ7AJ-<F- NM:i:0 MD:Z:107 MC:Z:45S106M AS:i:107 XS:i:106 E00435:54:H3LH5CCXY:7:1224:28107:39809 65 chr1 10003 0 107M44S chrY 57217029 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JJFJJJJJJJJJJJJJJJJJJJJJJAJJJJFJFJFFFJJJJJJJJJJFJJJJJFAFFJFJJJ<FJJAF<JFFJJJ<77--<<AJAJJ<AJJ)-<FF<- NM:i:0 MD:Z:107 MC:Z:106M45S AS:i:107 XS:i:106 E00435:54:H3LH5CCXY:7:2120:24221:8112 97 chr1 10003 0 107M44S chr5 11233 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ7FJFJJJJJJFJJFJJJJFJJJ<JJ<AJJJJJ7<A7<AA<FFFA7 NM:i:0 MD:Z:107 MC:Z:45S106M AS:i:107 XS:i:106 E00435:54:H3LH5CCXY:7:2207:17949:72701 129 chr1 10003 0 108M43S chr12 133265125 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCAAACAGATCGGAAGAGCGGCGTGTAGGGAAAGAGTGTAGATCTCG AAAFFJJJJJJJJJJJJJJFFJFJAFJFJJJJJJJJJJJJFJJFFJ<AJJJJJJJJFJJJJJFJJFJJAJFJAJAAFAAA-7FJJFFFJF7AF7AA7JJ----7A---A-------)-AF---))--<<)-<-7-7<-7A---<--7<7-- NM:i:1 MD:Z:102A5 MC:Z:110M41S AS:i:103 XS:i:103 E00435:54:H3LH5CCXY:7:1112:23490:47140 145 chr1 10003 5 39S106M1I5M chr5 11305 0 CTACCCCCAACCCTACCCCTACCCCTACCCCTCACCCTGACCCTAACACTACCCCTACCCCTAACCCTAACCCTACCCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCC 77))7)-)--7)<)7)<7)7-)A7))7)JFA7)7A7-7---<-77--7A---A-A-7-F77-A-A---A-FF-7-7FF-7-FJA<--<J<77--AF-<7AJJJAJAJJJJJFJJJJJJJJJJJFJJJJJJJJJJJFJJJJJJJJJJFFFAA NM:i:6 MD:Z:8C3A5A17A17A56 MC:Z:151M AS:i:83 XS:i:78 SA:Z:chr18,10577,-,3M1I43M104S,57,3; E00435:54:H3LH5CCXY:6:1103:32146:38930 129 chr1 10004 0 5S104M1I29M12S chr13 114354196 0 CCTACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCGCAACCCTAACCAGAACCGTAACCCTAACCGAAACGCCAGCC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJFJJJJJFFFJJJFJJFJFJJJAFJJAFJJJJ7AAAJJF<F-FFF7AA7FF-7<FJFA<<7<A-AFF7<-A--A----7777FF<A--7--77--A---7---7-------)<)7) NM:i:5 MD:Z:5A109C0T4C11 MC:Z:131M20S AS:i:106 XS:i:104 E00435:54:H3LH5CCXY:6:1123:15473:6741 65 chr1 10004 0 4S102M1I44M chr3 198173900 0 GATCCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACGCCAACCCTAACCCTAACCCTAACGCTAACCCTAACCCGAACCCTAAGCGCAACCCTAACCCTCACCCCAACCCCAGGCCTAACCCCAACCC AA-A<AF--AAFJ-<FFJJAFJAF<FFF7-<<A7A<F<F-<F<F<7-<F7FFJ-F7-FA-<-7-77-7A7--<-7AAAJJJJ-7AFJA-7--77-7--77-7A-F7-7---777A--7--7<-7A----7<---7))-7))--77))7)A7 NM:i:12 MD:Z:55C1T21C13T9C13A4T5T1A0C8T5 MC:Z:50M101S AS:i:86 XS:i:84 E00435:54:H3LH5CCXY:6:1224:25134:61556 65 chr1 10004 0 106M45S chrX 156030509 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTCAACTCCAGTCACGAGGTTGATCTC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJFF<AFFJJFFJJJ7-7-AA7-7--7A-7-FFFJ<--7F--A77FJ-F--7<)---7F7< NM:i:0 MD:Z:106 MC:Z:111M40S AS:i:106 XS:i:105 E00435:54:H3LH5CCXY:6:2208:26027:17149 97 chr1 10004 0 106M45S chr5 10178 0 CCCTAACCGTAACCCTAACCCTAGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGGTCGGAAGAGCAGACGTCTGAACTCCAGTCACGAGGTTGATACC AAFFFJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFA<7AFJJFJJJJJ<J-<<JFJ-<AJJJJ<FJJFJJ<F<A<FAFA-7 NM:i:3 MD:Z:8C14A37C44 MC:Z:46S105M AS:i:91 XS:i:90 E00435:54:H3LH5CCXY:7:1109:17330:44872 129 chr1 10004 0 103M1I19M28S chrX 156030464 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAGCGCCAACCCGAACCCTAACCCCAAGCCCACCCGTAACCCTAACCAGAAA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFFJJFFFJJJFFJFJAAFJFFAA-<--7--7--7-----7-----7)-7-----))-)7)))))))7)-7777--7--77-- NM:i:3 MD:Z:101A8T11 MC:Z:151M AS:i:105 XS:i:104 E00435:54:H3LH5CCXY:7:1201:21836:41110 65 chr1 10004 0 115M36S chrY 57217156 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCCAACCCAAACCCTAACCTAACCCTAACCGCAAAAGTCTGCACGACCCCACCCCTGAACACCACC AAA-AJJFJJJJJJJFJJJJFFFJJJJFJJFJFJFJJJJAJJFJFJJJFFJF-FFFFJ7JJFFAJJJJJFJJJFJ<FAJJJJF-7A--7-7F7<7-7A--<<FJ-<<-7FA<----------------7--7----)---)))-7----77 NM:i:4 MD:Z:83A3T5T10C10 MC:Z:105M46S AS:i:95 XS:i:94 E00435:54:H3LH5CCXY:8:2202:29721:37295 65 chr1 10004 0 106M45S chrX 156030515 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACCCGTCTGAACTCCAGTCACGAGGTTGATCTC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJFJFJJAAJJJJA<JJJJFJJJJAJ7FFJJ7JFFFJJFJFAF-<-A-AFJF-<J-7--<FJJJJ-7F<<A--A7< NM:i:0 MD:Z:106 MC:Z:105M46S AS:i:106 XS:i:105 E00435:54:H3LH5CCXY:8:2217:2148:67023 65 chr1 10004 0 106M45S chr18 80262975 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCTC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJFJJF7AFFFJJJJJJJJJJJJJJJFJJJFJJFJJFFJFJFFJ-<FJJ7<FJJAJFA<JJAFFJJJJ<AAJA))<F<<F77 NM:i:0 MD:Z:106 MC:Z:105M46S AS:i:106 XS:i:105 E00435:54:H3LH5CCXY:5:2102:19309:14828 81 chr1 10004 0 11S140M = 10182 40 CCTAACCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTACCCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCC A<7--JJJ7)JFFF-7JJJF-<JJJJJ<<J<J7--JJJA<-JJF<F-JJAAFJJJF7FJJJAFFJJJA-F-JFA7--JFA77-JJA-F-JFF7F<JJA---JFA7<-JF<7--JJAJFJJJJJ<JJJJJJJJJJJFJJJJJJJJJJFFFAA NM:i:15 MD:Z:5A5A5A5A5A5A5A5A5A5A5A5A5A5A5A50 MC:Z:47M1D18M8D67M19S AS:i:65 XS:i:62 E00435:54:H3LH5CCXY:6:2222:15544:53487 81 chr1 10004 37 11S140M chr3 10595 0 CCTAACCCTACCCCTACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTACCCCTACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTACCCC JJFAAJF<-)JJJJ<JJJFJF<FJJJJFFJJJJJFJJFFA<JJJFAAJJJJFJJJF-AJFJJJAJJJJF--JJJJF-JJJAAAJJJJJAJJJJA7JJJAF7JJJJ<FJJJJJFJFJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJA-FAA NM:i:6 MD:Z:5A5A29A5A5A82A3 MC:Z:48M1I44M58S AS:i:111 XS:i:91 SA:Z:chr2,102232685,+,131S20M,6,0; XA:Z:chr12,-10126,26M1I14M1D9M1D9M5D57M1D35M,13;chr3,-10532,34M5D71M1I10M1D35M,14;chr18,-10002,15M1D60M1I17M1I22M1D30M5S,9; E00435:54:H3LH5CCXY:7:2214:28808:25833 113 chr1 10004 5 5S58M1D57M1D29M2S chr22 50808362 0 TTAACCCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTNACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTA --)<AF<-<--JAF7-JJFAF<JJ<<---JJFFA-JJF7<FJJF-#JJJJAAFJJJ-A7JJFAAJJJJJJJJJFJJJJJAJJJJJJFAJJJJJJJJFJF-JJJJJFJJJF-JJJJJJJJJJJJJJJFJJJJJJJJJJJJFJJJJJJFFFAA NM:i:4 MD:Z:23A16A17^A57^T29 MC:Z:60S22M1D69M AS:i:123 XS:i:118 E00435:54:H3LH5CCXY:7:2223:24312:30738 129 chr1 10005 0 83M1D57M2D11M = 248945975 248935971 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCTTAACCTAACCCTAACCTTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<FJFFJ7FJ<AF7JJF<<AJJJJJJJFJJJJJJJF7FFJFJJJJJJJFJJJJ<FJJFJFJJ<JFJJAFAJ-<FAAF<F7-AF-AAJJ-7F--- NM:i:6 MD:Z:79C3^C13C5C37^AC11 MC:Z:82M2D17M1D28M1I23M AS:i:121 XS:i:120 E00435:54:H3LH5CCXY:8:1121:30888:52572 129 chr1 10005 0 116M1D18M17S chr12 133265169 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCTACCCTACCCCTACCCTAACCCTAACCCTACCCCCAAGATCGGAACG AAFFFJJJJJJJJJJJJJJFJJFJJJJF<JFFJ<<FFJJFAJJJJJJJFJ<FFAFJ<7--A7FAFFJFAJJJFJAAAA-FF7-77-7-7FJFAF<AJ----A<---A<<<J)7<7<<))7-----<7F7<7---)-)7)--)7--<)-7)) NM:i:4 MD:Z:98T5A6A4^A18 MC:Z:23M1D11M1D107M10S AS:i:112 XS:i:110 E00435:54:H3LH5CCXY:8:2203:26626:4052 65 chr1 10006 0 104M47S chr18 80263071 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCGCGATGTTGATCTCGT AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJAFJFJJJJFJJJJF<JJJJJFJJFJFFJJJFJAJFJJJJJJFJJFJFJJF77<AJJFFJFAJJ7FJA)F-<77JJFA-7 NM:i:0 MD:Z:104 MC:Z:105M46S AS:i:104 XS:i:103 E00435:54:H3LH5CCXY:5:2117:24444:45347 177 chr1 10006 6 50M6I50M1I44M chr13 114354168 0 CTAACCCCAACCCCCACCCTACCCCTAACCCTAACCCTAACCCTAACCCTTGCTCCGACCCCAACCCAAACCCTAACCCTAACCCTAACCCTCACCCTACCCCTAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC --)))<7)))))))-7A)))))F<--7-A7-7--7A-7--7-7---77----7----7A7----FA7--JAA7--FFFA7--JJFF<-<A77--F-JA--F--<-7JJA-JF77----A7AF-F--F-FJ<FF-JJAAA7-7JFFF-<A-- NM:i:16 MD:Z:7T5T0A6A28A4T5T24A6A50 MC:Z:151M AS:i:80 XS:i:74 XA:Z:chr3,-10409,21M1I29M5I43M1I7M5D44M,19;chr1,-180751,56M2D36M3D17M3D42M,20; E00435:54:H3LH5CCXY:7:2211:9871:33885 81 chr1 10006 5 18S24M6I76M1I26M chr17 113258 0 CTAAACCTACCCCCAACGCTAACCCTAACCCTAACCCCAACCACCACGCTAACCCTAACCCTAAGCCTAAAGCTACCCCAAACCCTAACCCTCACCATAACCATAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCC 7-7--)7)7))-))7--------7-7-A-7---F7-7-A7-----77-A<7-7---7---<----A7A<---7-------7-7FFJJ77F7---77--<7<----<<<<-JF7F7F<-<---AJJJF<F-FAAFJ-JAFJ-JJAJFFFAAA NM:i:16 MD:Z:19T20C5C0C3A3T12A3C5C47 MC:Z:45M1I15M90S AS:i:62 XS:i:55 XA:Z:chr22,+50808362,12M1I90M48S,9;chr15,+101981014,6M1D6M1D57M1I33M6I42M,21;chr12,-10271,42M4D3M3D24M5I24M1I25M1I26M,24; E00435:54:H3LH5CCXY:6:2101:25438:4069 145 chr1 10007 0 34S90M1D27M = 10015 -110 CCTTTCCCTACACGACGCTCTTCCGATCTACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAAGCCTAAGCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCAACCCTAACCCTAACC -<--7AAF7AAA<7<A-AFF<JJFFFAJJJJFF<77AAA<FA<JJFFFAFAFA<-JJFA<FJJF7AFJFF<J7<FA--FJJAA7<JJFAJJJJJJFFJJJJFFJJJAAAJJJFF7JJJJAFJJFFFJJJJJJJJJAFJJJJJFJJJFFFAA NM:i:3 MD:Z:33C5C50^T27 MC:Z:4M1I101M1D16M29S AS:i:100 XS:i:100 XA:Z:chr1,-10019,34S101M1D16M,3;chr22,+50808016,16M1D11M1D89M35S,4;chr22,+50808022,16M1D11M1D90M34S,5; E00435:54:H3LH5CCXY:8:1221:27123:71014 81 chr1 10007 1 8S55M1D57M1D29M2S chr18 10020 0 TTAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTA 7-F7FJFFA7-JJJF<<JJFFAFJFFF<-JFFF<-JJFAF7FFAF7AAJFF<FJAF7-7JFA7-FAFA7--7<-7--A<7-7-A<-<7JAA777<7<---JF<---JAF<-JJFF77JJFJFJJJFJFJJJJJJJJJJJJJJJJJFFFFAA NM:i:3 MD:Z:55^A6A50^T29 MC:Z:51M100S AS:i:122 XS:i:120 XA:Z:chr4,-10052,109M1D11M1D24M7S,4;chr3,-10404,8S25M1I29M2D88M,6;chr3,-10534,8S32M5D23M1D57M1D31M,11; E00435:54:H3LH5CCXY:5:2105:18852:69730 161 chr1 10008 1 4S12M2I41M1I64M27S = 10008 117 CTAAAACCCTAACCCTAAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCAGATCGGAAGAGCGTCGTGTAGGGAAA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJF7FJJJJAJJJFFFAJJJFJJJAFJAJ--77AFF-<7FJJF)A-))<-7<F-<7 NM:i:3 MD:Z:117 MC:Z:31S12M2I41M1I64M AS:i:102 XS:i:100 XA:Z:chr4,-190122830,27S16M1D90M7D14M4S,8;chr10,+10321,4S12M2I90M43S,2;chr18,+10095,5S11M2I54M1D36M1D11M32S,4;chr3,+10405,4S12M2I12M1I88M32S,5;chr4,-190122818,32S58M1I18M1D22M2I14M4S,5; E00435:54:H3LH5CCXY:5:2123:6258:52449 65 chr1 10008 15 44M4D29M1I12M1I50M14S chr13 114353892 0 TACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAAACCCTAAAACCCT AAFFFJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJFJJJFJFJJFJJJJJJJJJJJJJ<JJJA<J<JJFAAFJJJ<A<AAFFJJJJ-F7FJJJJFFJJ-<--FJ-----<<-AFAA----<AFF--<7AAJA- NM:i:7 MD:Z:0A43^CCCT91 MC:Z:91M1D12M48S AS:i:110 XS:i:99 SA:Z:chr20,56366347,-,2S20M129S,4,0; XA:Z:chr3,+10411,18M1I25M5D29M1I13M4D50M14S,12;chr1,+10062,44M3D29M1I25M1D14M1I23M14S,8; E00435:54:H3LH5CCXY:6:1212:21227:50181 97 chr1 10008 0 102M49S chr5 11048 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGACCGGAAGCGCACACGTCTAAACTCCAACCACGGGCTTGATCTCGTAT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFJJJJJJJJJ7-7-A--7AJ<FAA<--F------7--7-----7----)-7F-7--FFA- NM:i:0 MD:Z:102 MC:Z:46S105M AS:i:102 XS:i:101 E00435:54:H3LH5CCXY:5:2105:18852:69730 81 chr1 10008 1 31S12M2I41M1I64M = 10008 -117 GAGTTCAGACGTGTGCTCTTCCGATCTCTAAAACCCTAACCCTAAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACC JJJFJJJJJJJJJJJFF<FJJJJJFJFJJJJFFJJFJFJJJJ<JJJJJJJJFAJFJJJAJJJJAFJJJFJJFJFFJAJJFJF<JJJJFJ<JJJJFFFJJFF-JJFJFAJFJFFJJJJJJJJJJJF-JJJJ<<JJJJJJJJJJ<JJJFFFAA NM:i:3 MD:Z:117 MC:Z:4S12M2I41M1I64M27S AS:i:102 XS:i:100 E00435:54:H3LH5CCXY:6:1210:9780:4227 65 chr1 10009 0 101M50S chrX 156030425 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCTCGTATG AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJFJFJFJJJJFJ<JFJAFFJA7AJFFJJJFFJJJ<AF<FFAJAAFFFFA< NM:i:0 MD:Z:101 MC:Z:100M51S AS:i:101 XS:i:100 E00435:54:H3LH5CCXY:7:2121:30908:68816 161 chr1 10009 0 101M50S chr5 10849 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAACACCGTCGTGTAGGGAAAGAGTGTAGATCTCGGCGGCCGACC AAFFFJJJJJJJJJJJJJJJJJJJJFFJF<<FFJAFJ<FJF<JAAJ<-FFAJJFJ77F--AAF<<AJJJJA-AA-FA-7FAJAA-A7AA7FJJJ<-FFFFA-7-A77-7<<-<))7)))-7--------A--7<-<F<-<<7))))-)-<) NM:i:0 MD:Z:101 MC:Z:51S100M AS:i:101 XS:i:100 E00435:54:H3LH5CCXY:5:1203:1945:58761 129 chr1 10010 0 104M47S chrX 156030517 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCACAACCCTAACCCAAAAACAAACCGTAAACCTCACCCCACCCCCCAC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<<JJJJJJJJJJJJJJFFFJJJJJJ7FAJJF--FFJJ7<AAJJ-7FAFFF-AA--7---7---7-A---7-7--------77----7--77---<))))))<7))-- NM:i:0 MD:Z:104 MC:Z:109M42S AS:i:104 XS:i:100 SA:Z:chr1,178419283,-,25S20M106S,6,0;chr20,13531351,-,3M1D19M129S,0,1; E00435:54:H3LH5CCXY:6:1104:29427:43185 65 chr1 10010 0 4S18M1I82M46S = 248945980 248935971 GATCCCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGCCGCGCACACGTCTGAACTCCAGTCACGAGGTTGATCACG AAAFFFJJFJAFJFAJF<AF<FFJAJ<7FFFJJAFFJJJJJJJJJJJFFF--A-FJ7FJ7<A-FAJ<7FFF-AA7-<7-A--7<AJ7-7A<<---A---7FF7AFJ--AF7<-A--77<--7-<--7F77<<--7-----7-----7---7 NM:i:1 MD:Z:100 MC:Z:39M1I60M51S AS:i:93 XS:i:92 E00435:54:H3LH5CCXY:6:1118:30056:8939 161 chr1 10010 0 134M17S chr19 12986870 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCACCCCACCCACCCCCC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJFFFFJJJJF<JJJJJJJJJ7J<JJJFJFJJJFJ-AJJJ-AFJ-A<FJJ--AAFF-A--FF-AFFAJ-<-AAF---AA<)))-7))))-)7<7--F NM:i:1 MD:Z:95A38 MC:Z:129S22M AS:i:129 XS:i:123 SA:Z:chrX,27809567,+,131S20M,0,0; E00435:54:H3LH5CCXY:6:1206:15544:54963 97 chr1 10010 0 100M51S chr10 10185 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCTCGTATGC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAFJJFFFJJJJJJJJJJJJJ77JJJFJJJJJJJJ<FJ<FAFFF7<<-A-AJ NM:i:0 MD:Z:100 MC:Z:52S99M AS:i:100 XS:i:99 E00435:54:H3LH5CCXY:6:1222:12672:9941 161 chr1 10010 0 100M51S chr5 10502 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJJJJJJFFJJJJJFJ7AAJJA7--AAAA<)7-7<AFFJ<-<<F<JFJJ<-FFAF7F<))A7)-- NM:i:0 MD:Z:100 MC:Z:52S99M AS:i:100 XS:i:99 E00435:54:H3LH5CCXY:6:2103:19583:8904 65 chr1 10010 0 100M51S chrY 57217059 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGAAAATGAACACGTCTGAGTCTCAGTCTCCAGGATGATCGCGATTGC AAAFFJJAJ<JJFJFJJFFFJFJFJFJJJJJJJJJJFJ<AJAFJJJJF7FJJF-<AJF<FAAA<-A7A-<FJ7<<A-7-7--<FFF7J-AA77-A-AFJ-77-----<7-----777A<<<-------7FJ--77<F7-7F<<-7-))--- NM:i:0 MD:Z:100 MC:Z:100M51S AS:i:100 XS:i:99 E00435:54:H3LH5CCXY:6:2104:29376:33674 97 chr1 10010 0 4S18M1I82M46S = 10129 218 GATCCCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCTCG AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJ<FJJJJJJJJJFAFFJJF7AJJJA-7AJJF<FFJJJFJJF<A<F7<FJJF<AJJ7FJF7AFJJF<7FAJJFJJ<AF NM:i:1 MD:Z:100 MC:Z:51S49M1I50M AS:i:93 XS:i:92 E00435:54:H3LH5CCXY:8:1106:21745:65037 65 chr1 10010 0 100M51S chrX 156030515 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCCCGTATGC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJF<F-AFFFJA-A--AFFJ<J-<F-F7-<<AFJFJJJJJ7AJJJA-77))7<F NM:i:0 MD:Z:100 MC:Z:105M46S AS:i:100 XS:i:99 E00435:54:H3LH5CCXY:8:2118:6248:2575 65 chr1 10010 0 100M51S chr18 80263059 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCTCGTATGC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJFAJJJJFFFJJJJJJJJJ7AJJJJJAF<<AJ-A7FFFJJ<-7FAJ<-AFAAFF<<<<-AFJJFAFA7A<J NM:i:0 MD:Z:100 MC:Z:99M52S AS:i:100 XS:i:99 E00435:54:H3LH5CCXY:6:2123:2595:16182 177 chr1 10010 0 48S103M chrY 57217059 0 CCCCTCGTCCTCCCCCTACCCTAACCCGCTCCCTATCCCTAACCCTCCCCCTACCCCTAACCCTACCCCCAACCCTAACCCTACCCCTAACCCTAACCCTTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACC ))7)))))-)))-)))--7<--7))<-))-F<<-7---7--)--)-))FJA-7)AFA7---77-A-A77--FFJ<---<F777-JJA7-FFJF<7-JAA<-7FFJJF-FF<F-<JJJJF-JJJJFFJJJJFJJJJJF7JJJJJFJJFFAAA NM:i:5 MD:Z:5A11A3T13A16A50 MC:Z:89M1D58M4S AS:i:78 XS:i:78 E00435:54:H3LH5CCXY:7:1219:20862:1555 2193 chr1 10010 0 100M51H chr5 11165 0 CCCCATCCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCA )<))7-------AA--7-<)7)AF<-<-----<-AAAA--F<J<A-AAJF77-FFJF<JJJJFF7A7FFJJJJFA-FFJFFAJFJJJFJJJJJJJJJJJF NM:i:3 MD:Z:3T1A15T78 MC:Z:151M AS:i:89 XS:i:88 SA:Z:chr14,65636331,+,63M88S,14,2; E00435:54:H3LH5CCXY:5:1212:27011:65371 65 chr1 10011 0 99M52S chr12 133265213 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCTCGTATGCC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJFJJJJFFJFJJJJJJJFJJJJJJJJJJFFFJJJJJJJJJJFFJ7JJFFFFJJAAJJJJ NM:i:0 MD:Z:99 MC:Z:99M52S AS:i:99 XS:i:98 E00435:54:H3LH5CCXY:7:2118:23145:65072 97 chr1 10011 1 33M1D61M2I55M = 10186 273 CCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCTAACCCTAAC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFFJJJJAJFJJJJJJFJJA<JFJJFFJFJJ<A-AFF7AFJJF-<<AJJ--<FFFJ-77<FJ-7A7FF--AFJJ-7-7FF---FAJ--7FAF)-)7<FJ)7-7FF--7A NM:i:4 MD:Z:33^A99T16 MC:Z:58S51M5D42M AS:i:129 XS:i:126 E00435:54:H3LH5CCXY:5:1222:5923:35906 129 chr1 10012 0 99M52S chr12 133265159 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCACAACAAAAACAATAACCATAAGACTGACAGTACTCCGAGACCTAAACC AAFFFJJFJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJFJJFFFJJJFJ7<FAFAA<JJAJ-7<FJ-7FJF---AAA-77A<-F--AAF--7FJ----7J-7--7A----7-----7A---7<F7<---7---------))7)7)-7<--- NM:i:0 MD:Z:99 MC:Z:151M AS:i:99 XS:i:97 SA:Z:chr1,186325932,+,95S20M36S,1,0; E00435:54:H3LH5CCXY:8:1115:5315:42270 129 chr1 10012 0 98M53S chr18 80263077 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTCT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAAFF<-7F<AFJF)F)<7J-<FFAA-<-A-7<F<FJJFF<A))-AA7FJJF)) NM:i:0 MD:Z:98 MC:Z:99M52S AS:i:98 XS:i:97 E00435:54:H3LH5CCXY:8:1124:10784:21087 97 chr1 10012 12 69M1I3M5I17M1I46M1D9M chr5 10190 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACGCTAACGCTAACCCTAACCCTACACCTACGACTATCCCTTACCCTAACGCCTACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ--F-A-<-<7--F--FF-------AJ------A-7-------77--7--7--<---7-7---7---7-AA-AA-7-FFJJ77FFF--A<---AFJFJJ-7AJF<A--<< NM:i:13 MD:Z:47C5C21A4A12A41^C9 MC:Z:107S44M AS:i:88 XS:i:77 XA:Z:chr3,+10432,25M1D42M19I9M1I55M,24;chr1,+10060,47M1I21M1I3M5I21M1D25M1I26M,15; E00435:54:H3LH5CCXY:8:2205:3011:6038 161 chr1 10013 0 98M53S chr5 9999 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCTAACCCTAACCCGAACCCAAACTATCTGAATATCGATTCGTATGGAGAGAGTATGGATCTCGGAAGACCCCCC AAAAFJFJJJJJJFJJFAFJJJJFJJFJJFFJF<<FJJJJFAFJFJFJJF<F<--FJJ<F--AA-7-A-77A-AAAJ<---7---7FFJ--7A7<--7<---7A-7-----7---7--7---7--7)-------<---7-777)---7))) NM:i:2 MD:Z:72T17T7 MC:Z:50S101M AS:i:88 XS:i:86 E00435:54:H3LH5CCXY:8:2105:5446:38209 65 chr1 10014 0 96M1I41M1D13M chr22 50808359 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGACCCTAACCCAAACCCAAACCCTAACCCTAACCCGAACCCCAACCCCAACCTTA AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJA<F7FJF-7-AJ--7A<A7<-<7<-----7---7A7A-A-7AA-7AF<F7F-A---F-F<F)7)A-7A))FJ))7)<<--- NM:i:7 MD:Z:106T5T17T6^T5T4C2 MC:Z:88M63S AS:i:115 XS:i:114 E00435:54:H3LH5CCXY:5:2213:16315:34887 97 chr1 10015 0 95M56S chr12 10220 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCNTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACNCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCGCGTGTNCCGTCT AAFFFFFFFJFJJJJJJJJFFFJJJJJFFJJFJFJJJJJJJJJJ-#AFJFJFFFAAFFJJFJFJJJJJJJJJJJJAA<AJAAFFJJ#J<FFJFFFA<AJF-A<FJFJFJ-77FJJJJAFFFF7AJJ<F7JAF)-<7<A<FJA-F#-7F-7< NM:i:2 MD:Z:45C40C8 MC:Z:57S94M AS:i:91 XS:i:90 E00435:54:H3LH5CCXY:6:2101:25438:4069 97 chr1 10015 0 4M1I101M1D16M29S = 10007 110 ACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAAGCCTAAGCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCAACCCTAACCCTAACCAGATCGGAAGAGCCCACGTCTGAACTCCA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JJJJFJJJJJJJJJJJJJFJJJJFJJJJ<AJFJJFAJFJJJJFJJAJFFJJFFFFJ<FFJJJ<FFJFAAJ<JFF-F<JJJ)A<FA)AA77<FAJJ- NM:i:4 MD:Z:37C5C61^T16 MC:Z:34S90M1D27M AS:i:100 XS:i:100 SA:Z:chr19,43376126,-,5S19M127S,0,0; XA:Z:chr1,+10003,4M1I90M1D27M29S,4;chr22,-50808027,34S11M1D11M1D89M1I5M,5;chr3,+10412,4M1I13M1I28M1D75M29S,7; E00435:54:H3LH5CCXY:7:1104:27681:16850 161 chr1 10015 0 117M34S = 10015 117 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJFJJFJJFJJJJFJJJFJJJFFJJJFJFFJAJJJJJJJJJFFFJJ<JFJFJJJJJJJF7F<FJ77A-<AJ<-)7-A)7A)))-<<FA7FAAFA---7 NM:i:0 MD:Z:117 MC:Z:34S117M AS:i:117 XS:i:110 E00435:54:H3LH5CCXY:7:1206:2473:12314 161 chr1 10015 0 95M56S chr9 97753607 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCATCACTTGGTTAAGGTGGTGTTTTCCAGGTAAGATCGGAAGAGCGTCGTGTAGGGCA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFJJJJJJFJJ<J<FJJJJJJ<JFJJJJJFJFFJJJJJJJFFJAF7FFA-<-<F-7FAAJJ7F<JAJ)7<77<A77-F-7AA7)<)------))7 NM:i:0 MD:Z:95 MC:Z:120S31M AS:i:95 XS:i:94 SA:Z:chr9,97753607,+,94S31M26S,33,0; E00435:54:H3LH5CCXY:7:1213:4736:25587 161 chr1 10015 0 5M1D89M57S chrX 222346 0 ACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAACAGCGTCGTGTAGGGAAAGAGTTTAGATCTCGGTGGTCGCCGTGTCATT AAAFFJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJFAJJ<FJJJJJJJFJJJFJJJJJJJFFJFJJJJFJ7FJFAJJJF<FFJJ7FFFJF7A7--7A<AF-7F7--FA--FJJJJ-<FJAAF----7))7AF--JF)<7-7- NM:i:1 MD:Z:5^A89 MC:Z:62S89M AS:i:89 XS:i:89 E00435:54:H3LH5CCXY:7:2220:13149:10275 129 chr1 10015 0 95M56S chrY 57216993 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTTAAGGGAAAGAGTGTAGATCTCGTTGGTCGCCGTATCAT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFJJJFFJJJJF-A-AF-7JA-7<-7--)--AA-<7JA--F<-----77-<7------<7-)))77F- NM:i:0 MD:Z:95 MC:Z:94M57S AS:i:95 XS:i:94 SA:Z:chr5,41515510,-,21S19M111S,0,0; E00435:54:H3LH5CCXY:8:1114:14062:69625 65 chr1 10015 9 96M1I28M26S chrX 156030512 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCAACCCCTAACCCTAACCCGAACCCTAACCCTTACGCTCACCCGAACCCTAACGCTCA AA<<FFJFAAFJJJJJJFJJAJJFJJFFJJJJJJJJJJJFJ-FJ<AFF7JJF-F7AJJ<AFFJFAA-AJA-77<7A<AA-7FA-7AA7--7A<7---7-7--77-<---7----7A-A-7-7A7----------A<)-<A7)--7-7-7)- NM:i:3 MD:Z:70T40T12 MC:Z:131M20S AS:i:107 XS:i:101 XA:Z:chr22,-50807993,5S146M,9;chr4,-190122800,27S23M1I71M1D29M,6;chr18,-80262896,57S23M1D71M,1;chr22,-50808362,57S12M1I81M,1;chr4,-190122672,26S30M4I86M1I4M,9; E00435:54:H3LH5CCXY:8:2113:21663:6671 161 chr1 10015 0 95M56S chr5 10747 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGATCTCGGTGGTCGCCGTGTCAT A<AFFF7JJAJJFJFJJJJFAJJJJJFJFJJJJFJJJAF-<FFFJJJFJJJFJ7JJFJFAJFJFFJJ--F7FFJFF7F-AJJJF-7FJJ7AFAJA-7AA<--<-<<FJ-7)-)--77A--AF77-7A-)7--AFF7---))7<)--))77- NM:i:0 MD:Z:95 MC:Z:57S94M AS:i:95 XS:i:94 E00435:54:H3LH5CCXY:8:2207:18609:36469 129 chr1 10015 0 95M56S chr13 114354202 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGCCGCCGTATCCT AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJFJFJJJFF<AFJJJAAJJJJFJFFFFA<J--<7FJ<AJFA-<))-A-A-JF-FFJA<<<---<<-A<F)A-)--7<--<-7-- NM:i:0 MD:Z:95 MC:Z:94M57S AS:i:95 XS:i:94 E00435:54:H3LH5CCXY:7:1104:27681:16850 81 chr1 10015 0 34S117M = 10015 -117 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCC JJJJJJJFJJJJJJJJJJJFJJJFJJFFJJJJJJJFFJJF-JJJJJJJJJFJJJJJJJFJJJFJFJJJAF7JJJJFAJJJFFFJJJJJFJJJJFJJJJFFJJJJJJJJJJJJJJJJJJFJJJJF<JJJFFJJJJJFJJJJJJJJJJFAFAA NM:i:0 MD:Z:117 MC:Z:117M34S AS:i:117 XS:i:110 E00435:54:H3LH5CCXY:7:1206:2473:12314 2129 chr1 10015 0 26H95M30H = 10015 -95 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCA FJFJJJJJFFFFFJJFJF7JJJJFJJJJJJJJJJFF-JJJF7AJJJJJ<JJJFA7JJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ NM:i:0 MD:Z:95 MC:Z:95M56H AS:i:95 XS:i:94 SA:Z:chr9,97753607,-,120S31M,33,0; E00435:54:H3LH5CCXY:6:1201:25134:36065 161 chr1 10016 21 93M1I38M1D19M chr5 10106 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCTAACCCTCACCCTCACCCCAACCCTAACCCTAACCCTAACCCCAACCCTAAC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJ7AJAJJJAA7JJFA-<AA-<77FFJF<-FAF<A-AFA--7FJJF--AFA---7<----7FAA-7FAFF)7F<<7))-A<)))7<7-77-77-77FJA--7FF-))A-<7---7 NM:i:7 MD:Z:38C66A5A4T14^C9T9 MC:Z:118M1D10M1D23M AS:i:111 XS:i:99 E00435:54:H3LH5CCXY:7:2221:3620:54770 161 chr1 10016 0 95M56S = 10016 95 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JJJFJJJJJFJ<JFJFJJJFFJJFJFJJJA77FAFJJAJJ)<A<FA7--FF<-7<<--FFFJF<JAJJ)7A-)))7--- NM:i:0 MD:Z:95 MC:Z:56S95M AS:i:95 XS:i:93 E00435:54:H3LH5CCXY:8:2220:23307:72912 129 chr1 10016 0 94M57S chr18 80262898 0 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCATCGCAAGAGCGTCGCGCAGGGCATGAGCGTAGCTCACGGTGGTCGCCGCCTCTGTGA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJFFFJJJJJJJJJJJJJFJJJAF--------7---7-A))-)))-))))))7--)7F))---7)-)))7-)7)-))-)7)7-- NM:i:0 MD:Z:94 MC:Z:21M1D82M48S AS:i:94 XS:i:93 SA:Z:chr19,19033683,-,7S19M125S,0,0; E00435:54:H3LH5CCXY:7:2220:28798:22229 177 chr1 10016 2 19S58M1D74M chr18 80262943 0 CACCGAACCCGACCCCGATCCCTAACCCTACCCCTAGCCCTAACCCTAACCCTAACCCTACCCCTAGCCCCAACCCTACCCTACCCCCACCCCCAACCCTACCCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC )7A7)7---)))))-7)--77-7--JJF-7))7))))A---7FFA7---FF7---A7----A-77--F<7---J77--7JJAF77A7---FFA--7JFA-JA<<--<-A7--FJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFFAAA NM:i:11 MD:Z:11A5A23A5A3T6^A6A3T1A3T7A49 MC:Z:5S23M1D123M AS:i:75 XS:i:72 XA:Z:chr4,+190122748,132M19S,12;chr3,-10525,19S46M5D13M1D33M1D18M1I21M,15; E00435:54:H3LH5CCXY:7:2221:3620:54770 81 chr1 10016 0 56S95M = 10016 -95 GACGGCATACGAGATCAACCTCGTGACTGGAGTTCAGACGTGTGCNCTTCCGATCTCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA -FFJ<AAAJJJ<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJAJJJJJFJJJJFAJJJJJFJJJJFAJJJJJAJJJF7AJJJJJJJJJJJAJJJJFFJJJJFJJJJJJJJJJJJFJJJJJFJJJJJFJJJJJJFFFAA NM:i:0 MD:Z:95 MC:Z:95M56S AS:i:95 XS:i:93 E00435:54:H3LH5CCXY:6:1123:7831:57776 129 chr1 10017 0 97M54S chr18 80263072 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACGCTAACGCGACCCCTAACCCAACCCCCAACCCCACCCCTATCCCCCTCCCACCCCCAAACCCTACCCAAACCCCACACC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJ-F-F-A-7--7A----77-A---7-7)))-)))))))))--)))---<A))))-)))-)-))7<----)-)----7<))))<< NM:i:4 MD:Z:72C5C1T1A14 MC:Z:107M44S AS:i:77 XS:i:73 SA:Z:chr13,99988964,+,95S21M35S,0,0;chr14,94042484,-,18S20M113S,1,0;chr10,51683553,-,4S19M128S,0,0; E00435:54:H3LH5CCXY:7:1119:11820:26396 129 chr1 10017 0 93M58S chr12 133265219 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCGTCGTGTAGGGTAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJJJJJFJJJJFJJJJJJJJJFJJFFJJJFFJJJAFFJFF<JJAFF-----777FFJ<FAFJJJ-----7<-<A<AF<77-))-)7))<F-)A-77--- NM:i:0 MD:Z:93 MC:Z:93M58S AS:i:93 XS:i:92 E00435:54:H3LH5CCXY:6:1116:21460:3717 65 chr1 10018 0 108M43S chr4 190122729 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCAACCCTAACCCCAACCCAACCCCCCACCCTACCCCCAACCCCAACCCCACCCCACCCCCC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJ<FAJJJJFFJJFJJFJJJ-F-FJ--A-7<--<-JF7A-7A-<---7A----A-----77-7-7-7-7--<7-))-A)))))-)) NM:i:2 MD:Z:87A14T5 MC:Z:6M1D80M65S AS:i:98 XS:i:98 SA:Z:chr6,44530186,+,123S23M5S,0,0;chr16,16240995,+,109S21M21S,0,0; E00435:54:H3LH5CCXY:8:1209:31304:29384 65 chr1 10018 0 92M59S chr18 80263083 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCCCCAGGTTGATCTCGTATGCCGTCTTCT AAAFFJJFJJJJJJJJJJJJFJFJJJJJJFJFJJFJJJJJJJJJJJJJJJFJJJJJJJFFJJJFFJA<J<JJJJJJJJJJFJJJFFFJJJFJJAJJJFF7FFFJFJFFFFJJJAFA-FFFAFA----7A-7FAAF-F<FJ<FAJJAJ)F-< NM:i:0 MD:Z:92 MC:Z:93M58S AS:i:92 XS:i:91 E00435:54:H3LH5CCXY:7:2105:13088:54436 113 chr1 10018 2 129M1D14M3D8M chr21 9044022 0 CTAGCCCTAACCCTAACCCTAACCCTAACCCTAACCCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCACCCTAAC <A7AAJAA7-FFFFAJFFF-F<FJFAJAFFFFAJJJJFAJFJFAAJJJJFJ<JJFFFAJJJJFFJJJFFFJJJJJAJJJJJJJJJFAAJJJJJJJJJJJJJJJFFJJJJJJJJJJJ<JJJJFJJJJFJAJJJJJJJJJJJJJJFJJFFFAA NM:i:7 MD:Z:3A33T0A90^C14^CTA8 MC:Z:103S48M AS:i:122 XS:i:118 E00435:54:H3LH5CCXY:8:1116:19796:32056 113 chr1 10018 25 88M1I41M1D21M = 248945852 248935723 CTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAGCCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCC <A<-JFF<-7F-F-A7FFFFJJFFA<A-AFFAA-JFA-7-<FAA-<-77-7-F<--7-7F<--JA7<---A-F-JFJFA---AF<-7J777-F--FA<--AF<---JF<<--FFA7A<JJJJJJJJJJJJJJJJJJJJJJJFJJJJFFFAA NM:i:6 MD:Z:33A17A23A40A12^C21 MC:Z:112S39M AS:i:116 XS:i:102 E00435:54:H3LH5CCXY:5:1216:19339:72156 161 chr1 10019 0 91M1I16M43S chr10 10089 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAGCCAGACCCTAACCCAAACCCAGAGCCTAGCCCTCACCCTAAGCCGTAGCCTTACCAAAAACGG AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAJJJAJJJJJJJJJJJJJJ7---7--7--A7F-A----77<---7-----))A-))77))))))----<))-)7)-----A7-77--- NM:i:3 MD:Z:87C13T5 MC:Z:54S97M AS:i:90 XS:i:89 SA:Z:chr5,67835455,+,112S19M20S,0,0; E00435:54:H3LH5CCXY:6:2110:15331:17535 65 chr1 10020 0 90M61S chr18 80263083 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGGTTGATCTCGTATGCCGTCTTCTGC AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJ<JJFJJAFJJFJAFJJ7JFFFFFF NM:i:0 MD:Z:90 MC:Z:92M59S AS:i:90 XS:i:89

fanxinping commented 4 years ago

@sanjitsbatra I checked the records you provided and found no record can be used by Accucopy. Accucopy uses reads with MAPQ > 30. The MAPQ of most reads was 0 and I only found two reads (QNAMEs are E00435:54:H3LH5CCXY:6:2222:15544:53487 and E00435:54:H3LH5CCXY:6:2222:15544:53487) are valid. However, FLAGs of the two reads are 113 and 81 respectively, which means they are not proper pair and will be filtered out. So, Accucopy found 0 valid fragments.