KeepLearningBigData
KeepLearningBigData

基因数据处理50之cs-bwamem、bwa、snap、bwa-mem与art比较

直接看结果：

（1）art仿真数据：

hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ cat G38L100c50Nhs20.aln 
##ART_Illumina  read_length 100
@CM art_illumina -ss HS20 -i GRCH38chr1L3556522.fna -l 100 -c 50 -o G38L100c50Nhs20 -rs 1464918709
@SQ chr1  AC:CM000663.2  gi:568336023  LN:248956422  rl:Chromosome  M5:6aef897c3d6ff0c78aff06ac189178dd  AS:GRCh38  248956422
##Header End
>chr1   chr1-50 93465784    +
TTCCACAATAGTTGAACTAATTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAA
TTCCACAATAGTTGAACTAATTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAA
>chr1   chr1-48 228133745   +
ATCATTGTATGCCACAGAAATAATTAAATTTCCTTGTCAACTGAGACATTATTATTAGGCACTCTCACCAGATCTTTACCCATGGCCATTTAAAGTGTGG
ATCATTGTATGCCACAGAAATAATTAAATTTCCTTGTCAACTGACACATTATTATTAGGCACTCTCACCAGATCTTTACCCATGGCCATTTAAAGTGTGG
>chr1   chr1-47 13772987    +
TTCAGTAATTCAGAATAACACATGAGGGAATGAATGAATGAATAAATAAAAAAAAAATGAATGAATAAATTAAAAAAAATTGTGTTTCAGGGAAGAAAAA
TTCAGTAATTCAGAATAACACATGAGGGAATGAATGAATGAATAAATAAAAAAAAACTGAATGAATAAATTACAAAAAATTGTGTTTCAGGGAAGAAAAA
>chr1   chr1-46 211481565   -
ATCCCGATCAGGAACCTGGTGCTCTTCCCCGGCTCTCCCAACTTGGGCAAAGTTGGAGGGGTCCTGAGGCCCGGCGGGCCGGGGAACAGGACCCCGACCC
ATCCCGATCAGGAACCTGGTGCTCTTCCCCGGCTCTCCCAACTTGGGCAAAGTTGGAGGGGTCCTGAGGCCCGGCGGACCGGGGAACAGGACCCCGACCC
>chr1   chr1-45 29056656    +
CTGGGATTACAGGTGCCCGCCACCATGCCCAGCTAATTTTTGTATTTTTGGTAGAGACAAGGTTTCACCATGTTGGCCGGGATTGTCTCGAACTCCTGAT
CTGGGATTACAGGTGCCCGCCACCATGCCCAGCTAATTTTTGTATTTTTGGTAGAGACAAGGTTTCACCATGTTGGCCGGGATTGTCTCGAACTCCTGAT
>chr1   chr1-44 49993892    +
CAATTTAGCCAAAACTGGCTAATCCTTTTACCAGAATCATTCCCATTGTTCAAGACCTATTTTAAGCTCCACTATCACCATAAAACTTTCCCGATCAGTT
CAATTTAGCCAAAACTGGCTAATCGTTTTACCAGAATCATTCCCATTGTTCAAGACCTATTTTAAGCTCCACTATCACCATAAAACTTTCCCGATCAGTT
>chr1   chr1-43 54241817    -
TTGCAGACCTTTTATTGATTGTGAAATAACCCAAGAGAACACACATGGAACCATTTTTAAAGTATCATCAAATTTAAATATGATATTATTAAAACATATT
TTGCAGACCTTTTATTGATTGTGAAATAACCCAAGAGAACACACATGGAACCATTTTTAAAGTATCATCAAATTTAAATATGATATTATTAAAACATATT
>chr1   chr1-42 35706202    +
CAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACGTGCCACCATGCCTGGCAATTTTTGTATTTTTAGTACAGATGGGG
CAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACGTGCCACCATGCCTGGCAATTTTTGTATTTTTAGTACAGATGGGG
>chr1   chr1-41 92473985    -
GGTGGGCCCATACACACAGGCACCAGGATATACCCCCGCCTGCATCCACATGGACACGTGCCCACGTTGCATGTACACGCAGACCTGCCTATGCACACAC
GGTGGGCCCATACACACAGGCACCAGGATATACCCCCGCCTGCATCCACATGGACACGTGCCCACGTTGCATGTACACGCAGACCTGCCTATGCACACAC
>chr1   chr1-40 27177039    -
GAACCATTTGGCTGAGCCCAGCACTCTGCCCATGGTCCATGCACCCCTTGACCCTGACATCAGCAAAGCAGTCCCCATCACCAAAGTGCTATGTGCCATG
GAACCATTTGGCTGAGCCCAGCACTCTGCCCATGGTCCATGCACCCCTTGACCCTGACATTAGCAAAGCAGTCCCCATCACCAAAGTGCTATGTGCCATG
>chr1   chr1-39 245060718   -
TCTTGACATTTTGGAGTTGACACCTTGGAGGTGGTTAATCCATGACGAAACTGAAGCTAAGCCGATCTCATGTTTTGACTCCTGTCAATCCGGAGAGGAC
TCTTGACATTTTGGAGTTGACACCTTGGAGGTGGTTAATCCATGACGAAACTGAAGCTAAGCCGATCTCATGTTTTGACTCCTGTCAATCCGGAGAGGAC
>chr1   chr1-38 215781397   -
TACATATACATATACATATACATACATGTGTGTGTGCATATATATGTATATGTGTGTATATATATATATATATATATATACACACATATATGTATGTGTG
CACATATACATATACATATACATACATGTGTGTGTGCATATATATGTATATGTGTGTATATATATATATATATATATATACACACATATATGTATGTGTG
>chr1   chr1-37 42831546    -
AACAACGTATGTCCACACAAAAACTTGCACATGAATGTTCACTAGCAGCATTATTTGTAACCTGCCCAAGGTGGAAACAACCCAAATGTCTATTGACTGA
AACAACGTATGTCCACACAAAAACTTGCACATGAATGTTCACTAGCAGCATTATTTGTAACCTGCCCAAGGTGGAAACAACCCAAATGTCTATTGACTGA
>chr1   chr1-36 181673625   +
TCCACTGCCCAGAAAGAGGACATCCCTTATAGGGCCAGCGGATGGAAGCCATGGGCTGGGCAGGACATTCCTGTCCCAACCCACATGGCAGCTAGAGTCC
TCCACTGCCCAGAAAGAGGACATCCCTTATAGGACCAGCGGATGGAAGCCATGGGCTGGGCAGGACATTCCTGTCCCAACCCACATGGCAGCTAGAGTCC
>chr1   chr1-35 96851543    -
GTTGTGACCTCCCAACCCCCACAGAGGTTCACGTGTTGAAGTCTTAACCCTCAGTACCTCAGAATGTAATCATATTTGAAGATATGGTATTTATAGAGGT
GTTGTGACCTCCCAACCCCCACAGAGGTTCACGTGTTGAAGTCTTAACCCTCAGTACCTCAGAATGTAATCATATTTGAAGATATTGTATTTATAGAGGT
>chr1   chr1-34 13267476    +
ATACAGGGAAGGTTTTAATCTGTTTCAGACATTAGAAATACATATATTTATATATGGTATCTTTATTGGAGAACCTTTGGCCACATCAAAAGTATCAAAA
ATACAGGGAAGGTTTTAATCTGTTTCAGACATTAGAAATACATATATTTATATATGGTATCTTTATTGGAGAACCTTTGGCCACATCAAAAGTATCAAAA
>chr1   chr1-33 48968232    +
GAATAGTAGGCAATAAACAAAGAGAGCAACTTAGGAGCCAGATCACATGTGGCCTCTCGAGCAATATGGTAAAAGTTCTGGACTTCATTCTAGGTGAATG
TAATAGTAGGCAATAAACAAAGAGAGCAACTTAGGAGCCAGATCACATGTGGCCGCTCGAGCAATATGGTAAAAGTTCTGGACTTCATTCTAGGTGAATG
>chr1   chr1-32 88980622    +
TAGTTCAGTAAACTATTTATCAAACAGGTGTCTGGTCATTTTAACATACTCCTTGCTTTGAACAATATTCATTCATATTTGGTACAAACTCTATATCCTA
TAGTTCAGTAAACTATTTATCAAACAGGTGTCAGGTCATTTTAACATACTCCTTGCTTTGAACAATATTCATTCATACTTGGTACAAACTCTATATCCTA
>chr1   chr1-31 21950729    -
TTCCCAAATTAACTAACTTCACCTAGGTTGTGAGTATTGCAGCGTCTTATTTCTAATCCCAGTACTACTATTGGTGTGAGTCAGTAAAGATGCCTGGTGA
TTCCCAAATTAACTAACTTCACCTAGGTTGTGAGTATTGCAGCGTCTTATTTCTAATCCCAGTACTACTATTGGTGTGAGTCAGTAAAGATGCCTGGTGA
>chr1   chr1-30 9852128 +
TGTGAAATGGAGTCAGCAGAGTGAGCCGGCCTCCACTCAGTGAGCCGGGTCTCCCCCACAGCCGGCATGTGCTGACCTCCTTCCAACTGCTCTACCAAGA
TGTGAAATGGAGTCAGCAGAGTGAGCCGGCCTCCACTCAGTGAGCCGGGTCTCCCCCACAGCCGGCATGTGCTGACCTCCTTCCAACTGCTCTACCAAGA
>chr1   chr1-29 92558892    -
CAGCCTGGGCAACATGGTGAAACCCCGTCTCTACTGAAAATACAAAAATTAGCCGGGCGTGGTGGCAGGTTCCTGTAATCCCAGCTACTCGGGAGGCTGA
CAGCCTGGGCAACATGGTGAAACCCCGTCTCAACTGAAAATACAAAAATTAGCCGGGCGTGGTGGCAGGTTCCTGTAATCCCAGCTACTCGGGAGGCTGA
>chr1   chr1-28 191969685   -
ACATCACCTACTGGAATTGAAACATGGTTCCTAAGAATGGGCTCTCATGGCCAGGATCCAAAAGGAAGGCCATGGTTCCACAAGGAGACCTGTTCTGAGT
ACATCACCTACTGGAATTGAAACATGGTTCCTAAGAATGGGCTCTCATGGCCAGGATCCAAAAGGAAGGCCATGGTTCCACAAGGAGACCTGTTCTGAGT
>chr1   chr1-27 76941125    -
GGATATCAACAAACTGATTCTAAGTTTTGTATGGAGAAGCAAAGAGCCCAGGATAGCCAACACAATATAAAAGAAGAACAAAGCTGGAGGACTGACACCT
GGATATCAACAAACTGATTCTAAGTTTTGTATGGAGAAGCAAAGAGCCCAGGATAGCCAACACAATATAAAAGAAGAACAAAGCTGGAGGACTGACACCT
>chr1   chr1-26 233336762   +
AGATATACAGCAAAGTTTGAAAGCTACAGTTCTGAGGACCAGATTTATGGATTCCTTCTTATATGTTATCTGGGTTGATATAGAAATTCTTCCATGGCTA
AGATATACAGCAAAGTTTGAAAGCTACAGTTCTGAGGACCATATTTATGGATTCCTTCTTATATGTTATCTGGGTTGATATAGAAATTCTTCCATGGCTA
>chr1   chr1-25 96853884    +
GCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGGTGAGCATTTTTTCATGTGTTTTTTGGCTG
GCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGGTGAGCATTTTTTCATGTGTTTTTTGGCTG
>chr1   chr1-24 235841968   +
GTTGGCTACTAGCTTAGCAGAGGTGGAAAACCATGAATTTCTGGTGGTATGGATTTTTTCAGCTATTTCAGATTCACCAGCAGGATTCAGCTGCTTGGGT
GTTGGCTACTAGCTTAGCAGAGGTGCAAAACCATGAATTTCTGGTGGTATGGATTTTTTCAGCTATTTCAGATTCACCAGCAGGATCCAGCTGCTTGGGT
>chr1   chr1-23 96545357    +
AGTGAAAAAGGCTGGCTGCCCTTCAATATCATCTTCAAATGTTAACAACACTGAATATTAATAAATTTCCTTTAGCGAATAATGAATCCAGCCTTCCTTA
AGTGAAAAAGGCTGGCTGCCCTTCAATATCATCTTCAAATGTTAACAACACTGAATATTAATAAATTTCCTTTAGCGAATAATGAATCCAGCCTTCCTTA
>chr1   chr1-22 80270678    +
TTGTACACCCTATTTCTGACCAGAAGAAGGAGCATTTTGCTTTTTGCCAAATGAGAAGTGCATTCTGGAAACACTTGATGCCTGCACCACACCTCGAGTT
TTGTACACCCTATTTCTGACCAGAAGAAGGAGCATTTTGCTTTTTGCCAAATGAGAAGTGCATTCTGGAAACACTTGATGCCTGCACCACACCTCGAGTT
>chr1   chr1-21 35923260    +
CTAAGCAGCAGTGTTTTTGGATACTTTTTTTTTCTGTTTGTGAATAAGGCCAGCACTCAAGATGGGCAGCCAAGGGTGCACTGACTATTAGCTGGCCCAT
CTAAGCAGCAGTGTTTTTGGATACTTTTTTTTTCTGTTTGTGAATAAGGCCAGCACTCAAGATGGGCAGCCAAGGGTGCACTGACTATTAGCTGGCCCAT
>chr1   chr1-20 136467133   -
ACTGTGCCTGGCCTTTTTTTTTCTTTTTCTTTTTTTTACACTCTCATGTTAAAAAAAAATCTGTCCTTGTTACTATATAGATGTGCATAGTTCATTCCCT
ACTGTGCCTGGCCTTTTTTTTTCTTTTTCTTTTTTTTACACTCTCATGTTAAAAAAAAATCTGTCCCTGTTACTATATAGATGTGCATAGTTCATTCCCT
>chr1   chr1-19 160371243   +
AGGCCCTGGGCACAGGCAGAGAGCCCACCGGCTGGTCATGAGGGCCTCTTCCTTTCTCTGACCCAGGCACCTCGAGGGCTATTCTCCTGGGTTCCTTCCG
AGGCCCTGGGCACAGGCAGAGAGCCCACCGGCTGGTCATGAGGGCCTCTTCCTTTCTCTGACCCAGGCACCTCGAGGGCTCTTCTCCTGGGTTCCTTCCG
>chr1   chr1-18 69100488    -
AGTGCTGGTATTACAGGTGTGAGCCACTGTGCCTGGTCAGCAGTACTTCACTGCTATAATTTTACAACTTTTAAAGATAACCTAATTTATTTTAATTGCT
AGTGCTGGTATTACAGGTGTGAGCCACTGTGCCTGGTCAACAGTACTTCACTGCTATAATTTTACAACTTTTAAAGATACCCTAATTTATTTTAATTGCT
>chr1   chr1-17 41500328    -
GGAGTGAAATAATGAAAATATATATATTTCTTAATTTTTTGTTTTCATAATTGGAAAGTGACCTATAGGTCACTCTTTAACCTTTCCAATCATAAGAACC
GGAGTGAAATAATGAAAATATATATATTTCTTAATTTTTTGTTTTCATAATTGGAAAGTGACCTATAGGTCACTCTTTAACCTTTCCAATCATAAGAACC
>chr1   chr1-16 114154602   +
TGTATCTTTCTGCTAAGCATAACAAGAAAGACAGAAAGCTCAACGGGAGGATTGAGGCTAGACTTAAAGTAGAGATCCCCTCAGAAACTGTGGAGTGAGG
TGTATCTTTCTGCTAAGCATAACAAGAAAGACAGAAAGCTCAACGGGAGGATTGAGGCTAGACTTAAAGTAGAGATCCCCTCAGAAACTGTGGAGTGAGG
>chr1   chr1-15 79188743    -
TGCCTAGAGTGTCAAACATCCTTTATCATTTTAAAATCTAAACTCCAAAATCCTTCCTATTAGGGCCTTTCCTCCCTCGTTTCCTTTCCTCTCCCCCACC
TGCCTAGAGTGTCAAACAACCTTTATCATTTTAAAATCTAAACTCCAAAATCCTCCCTATTAGGGCCTTTCCTCCCTCGTTTCCTTTCCTCTCCCCCACC
>chr1   chr1-14 117644125   +
GCATTTCATTGTGGACTAATTTTCCCCCACTATTGAGGGAAGACCCTTTTGAGTACTCTATCTGATGCCCCATGAATGATAAAGTTTTATACTCTGGCTG
GCATTTCATTGTGGACTAATTTTCCCCCACTATTGAGGGAAGACCCTTTTGAGTACTCTATCTGATGCCCCATGAATGATAAAGTTTTATACTCTGGCTG
>chr1   chr1-13 104996993   +
TTCTTGCTGGAACACATGGTTTCACCTTTACCTTCACCCACAGCCCAATGTGCATCAATATGGAGATAATGCAGTTCCATTTGTACCTCTTTGTGATTCA
TTCTTGCTGGAACACATGTTTTCACCTTTACCTTCACCCACAGCCCAATGTGCATCAATATGGAGATAATGCAGTTCCATTTATACCTCTTTGTGGTTCA
>chr1   chr1-12 140338618   -
TTTCTTCATTTGGTTTTCAGGACAGGACTCTGCTTTGCTTTCCTCCTCTGATCACACTGGTGGTTTCTTTGCTCATTCTTCTTCCCAATCTCCCCGACCT
TTTCTTCATTTGGTTTTCAGGACAGGACTCTGCTTTGCTTTCCTCCTCTGATCACACTGGTGGTTTCTTTGCTCATTCTTCTTCCCAATCTCCCCGACCT
>chr1   chr1-11 176870999   -
GCAGACTCAATAATTGGCTATGATAACAAATACTCTTTCACATACCAGGGACAACAATATTAACTCTGGAATATTATTTTAAACATTTTCAAGGCTAGTA
GCAGACTCAAGAATTGGCTATGATAACAAATACTCTTTAACATACCAGGGACAACAATATTAACTCTGGAATATTATTTTAAACATTTTCAAGGCTAGTA
>chr1   chr1-10 34644993    -
AGTCCAGAATTCTGAGTCTGTGAGTTTACACCTTCCAACAGTGATAATCAGATATCAAGCTTGAAGACTACCAACAAAAGTGGACCAAATAGGGATCATC
AGTCCAGAATTCTGAGTCTGTGAGTTTACACCTTCCAACAGTGATAATCAGATATCAAGCTTGAAGACTACCAACAAAAGTGGACCAAATAGGGATCACC
>chr1   chr1-9  152012628   +
AAGCAATTCTCTTGCTTTAGCCTCCCGAGAAGCTCGGATTACAGGCATGTCCACCACACCCAGCTAATTCTTTTGTATTTTTAGTAGACATGGGGTTTTG
AAGCAATTCTCTTGCTTTAGCCTCCCGAGAAGCTCGGATTACAGGCATGTCCACCACACCCAGCTAATTCTTTTGTATTTTTAGTAGACATGGGGTTTTG
>chr1   chr1-8  79478959    +
GGCAACACTTGAGAACACAAAGTGAGTTCTCACTTTGGGCGGTGGTTTCAGGCTTCAGGGTGGAGTTTTGTCAGGAACCCACCCTTTTCTGCCTAGAATT
GGCAACACTTGAGAACACAAAGTGAGTTCTCACTTTGGGCGGTGGTTTCAGGCTTCAGGGTGGAGTTTTGTCAGGAACCCAACCTTTTCTGCCTAGAATT
>chr1   chr1-7  178190760   +
GTAGCCGGAATAAACAGTCACTGTGAGTTGTCCATTTTAGAGCATAGGTTTTTAGGTGGTGAAGACCTGTCCTTAGTTGAATTTGTATGTGAATTAAACT
GTAGCCGGAATAAACAGTCACTGTGAGTTGTCCATTTTAGAGCATAGGTTTTCAGGTGGTGAAGACCTGTCCTTAGTTGAATTTGTATGTGAATTAAACT
>chr1   chr1-6  42572410    +
AACCCTTTATCAGGTATGTATTATAAACATCGACTCTGTGGCTTGCATTTTCATTCTCCTTATATATCTTTTGATGAATCAAAGTTTTTAATTTTAATAT
AACCCTTTATCAGGTATGTATTATAAACATCGACTCTGTGGCTTGCATTTTCATTCTCCTTATATATCTTTTGATGAATCAAAGTTTTTAATTTGAATAT
>chr1   chr1-5  153186634   +
GTCTTGACTCTTTATCCACTTTGCCAGTCTGTGTCTTGTAATTGGGGCATTTAGCCTATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCT
GTCTTGACTCTTTATCCACTTTGCCAGTCTGTGTCTTGTAATTGGGGCATTTAGCCTATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCT
>chr1   chr1-4  127714516   -
AGTGGAAATAATACTCGTCAACATATGCCTTTCAAAAAAATTTTTTTTCATATTTTAAATTTACCTTTACTACCTATTTATTTGGTTCAAGGCTCCATTT
AGTGGAAATAATACTCGTCAACATATGCCTTTCAAAAAAATTTTTTTTCATATTTTAAATTTACCTTTACTACCTATTTATTTGGTTCAAGGCTCCATTT
>chr1   chr1-3  84685020    +
TATTATTAAAACTATAAATGGACCAATTAAACAAACGTGTCATGAGCCAAGGAATATAAACTAATTCTTTACACCTGAAGTCCTTTAAAATGCTTTAAAT
TATTATTAAAACTATAAATGGACCAATTAAACAAACGTGTCATGAGCCAAGGAATATAAACTAATTCTTTACACCTGAAGTCCTTTAAAATGATTTAATT
>chr1   chr1-2  62477841    +
TAGGAAAATGGAGAAACTTTAATATGAAATCTTCCTGTTTTTCACATTATGTTTAGATTGTTACAGCATAAAATTTCCAAAACATTGCAAAAAGTTTTAA
TAGGAAAATGGAGAAACTTTAATATGAAATCTTCCTGTTTTTCACATTATGTTTAGATTGTTACAGCATAAAATTTCAGAAACATTGCAAAAAGTTTTAA
>chr1   chr1-1  11355149    +
ATTTATTGGCTGTCTTTCAGGCACATTTTAGCTGTCATCCAACATTCTCAACCTTAGTCCCCTTCTCTGGGCTAAGGGGAGAATGATGGTCCTACCCCAG
ATTTATTGGCTGTCTTTCAGGCACATTTTAGCTGTCATCCAACATTCTCAACCTTAGTCCCCTTCTCTGGGCTAAGGGGAGAATGATGGTCCTACCCCAG

（2） bwa

hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ cat G38L100c50Nhs20.sam
@SQ SN:chr1 LN:248956422
@PG ID:bwa  PN:bwa  VN:0.7.13-r1126 CL:bwa samse GRCH38chr1L3556522.fna G38L100c50Nhs20.sai G38L100c50Nhs20.fq
chr1-50 0   chr1    93465785    37  100M    *   0   0   TTCCACAATAGTTGAACTAATTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAA    @@CDFDFDHFHGHIJH:IJJJ(JJE?JDIDEJIB@FGJIGBHJ()HG8(CIICGFFHEH=GI3@&@DD58FADDACHDDHFCD8D,DCCXT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-48 0   chr1    228133746   37  100M    *   0   0   ATCATTGTATGCCACAGAAATAATTAAATTTCCTTGTCAACTGACACATTATTATTAGGCACTCTCACCAGATCTTTACCCATGGCCATTTAAAGTGTGG    @>CFFFFFH<@D(:EFDDC@;DDAC95(D?BD    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:44G55
chr1-47 0   chr1    13772988    37  100M    *   0   0   TTCAGTAATTCAGAATAACACATGAGGGAATGAATGAATGAATAAATAAAAAAAAACTGAATGAATAAATTACAAAAAATTGTGTTTCAGGGAAGAAAAA    CC@F(FFFDFH.HDHIGI(JIIIGGIEEJIIIHJJHHH3IJJIIJ3=EI>JDIGH((IBJCIEHGD>;J@HF+DC)CCCADBDBD+BDDDD5B5DDDE(C    XT:A:U  NM:i:2  X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:56A15A27
chr1-46 16  chr1    37474758    37  100M    *   0   0   GGGTCGGGGTCCTGTTCCCCGGTCCGCCGGGCCTCAGGACCCCTCCAACTTTGCCCAAGTTGGGAGAGCCGGGGAAGAGCACCAGGTTCCTGATCGGGAT    (5CBACDDD>FBDDDDDEC:CE(CBDFDDHEFH;FGEFHGHDGJJJDIGI:JEHJ=JJJJJH8CI?JJJG9JIII>IJIIGJ=EIJGAHHHHFFDFDCC?    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:22C77
chr1-45 0   chr1    29056657    37  100M    *   0   0   CTGGGATTACAGGTGCCCGCCACCATGCCCAGCTAATTTTTGTATTTTTGGTAGAGACAAGGTTTCACCATGTTGGCCGGGATTGTCTCGAACTCCTGAT    B@@FFFFFHHG)HIJJJJBJIJCJHGJIBFJJI3IIHDF@JIAJ9JJJIJJBIJJ?BJID8F:HFHA(+D>J>CG>7D=DDFF@EDC3D@BD@B    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-44 0   chr1    49993893    37  100M    *   0   0   CAATTTAGCCAAAACTGGCTAATCGTTTTACCAGAATCATTCCCATTGTTCAAGACCTATTTTAAGCTCCACTATCACCATAAAACTTTCCCGATCAGTT    C@CFFFFDHHHHH@JJJHI)IDIBIJA:HJHFJJJIJGGJJIIIIHGGJJGH<(IIIJI?ICDG;CDHFHCDCCB?FDDED:CD:>DD5C&DDCD    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:24C75
chr1-43 16  chr1    194714506   37  100M    *   0   0   AATATGTTTTAATAATATCATATTTAAATTTGATGATACTTTAAAAATGGTTCCATGTGTGTTCTCTTGGGTTATTTCACAATCAATAAAAGGTCTGCAA    CCCCDDC@E>CDCDDC>D9CD=C)CGC>E@7.HF)DIBJBJJ.JEJEJ@JJIIIIGD?@B    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-42 0   chr1    35706203    37  100M    *   0   0   CAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACGTGCCACCATGCCTGGCAATTTTTGTATTTTTAGTACAGATGGGG    CC@FDFFAHHGFHJIHJFJJII=@JEHIJIIJIJEJIJJHHGIJBBFJG6JJHJJGXT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-41 16  chr1    156482338   37  100M    *   0   0   GTGTGTGCATAGGCAGGTCTGCGTGTACATGCAACGTGGGCACGTGTCCATGTGGATGCAGGCGGGGGTATATCCTGGTGCCTGTGTGTATGGGCCCACC    D;CCDDCDCDDDCD:EDA@@CJJI,=FHJJIGJ7GEC?IGJJIFBBICHJEIJJHHAIJIJI.IJGJJGJJHHGHHFFFFFB=B    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-40 16  chr1    221779284   37  100M    *   0   0   CATGGCACATAGCACTTTGGTGATGGGGACTGCTTTGCTAATGTCAGGGTCAAGGGGTGCATGGACCATGGGCAGAGTGCTGGGCTCAGCCAAATGGTTC    DDBCDCDDDDDDD25F?DD@4I5HED?CAHGA?JJIIJB)IHFJJFCJII?@XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:39G60
chr1-39 16  chr1    3895605 37  100M    *   0   0   GTCCTCTCCGGATTGACAGGAGTCAAAACATGAGATCGGCTTAGCTTCAGTTTCGTCATGGATTAACCACCTCCAAGGTGTCAACTCCAAAATGTCAAGA    DD5CCAD&8DAD>D&FDDDCDBDD?6DD.FHDDIFE?@IDEGIBCGD?JFJ>JGBI,IJIF.JJIHJJJEIEGFJ=JJHJHHJFHIJHHHHHFFAFFC@B    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-38 16  chr1    33174926    37  100M    *   0   0   CACACATACATATATGTGTGTATATATATATATATATATATATACACACATATACATATATATGCACACACACATGTATGTATATGTATATGTATATGTG    CDDC(FBDC(AACBDDCBDDECEC5@H;HFDJFH>=FCHAHJFJ'H3JG9JFEHIJFDJJ9IJHEJIGJIJJJJJC;J?AJFJGEHFHDC>D?DDBDFB)DDDDDC5(9>F;G)FB84/AJE3JJIJIGIGJBBIGCJCJGJGHJIDJ>IB7IGJGEGCIIGFJJJEFHIIJHHF=HFF8=F??=    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:14C85
chr1-34 16  chr1    12934213    0   100M    *   0   0   TTTTGATACTTTTGATGTGGCCAAAGGTTCTCCAATAAAGATACCATATATAAATATATGTATTTCTAATGTCTGAAACAGATTAAAACCTTCCCTGTAT    D@CB?DEDCEDDD(DC>F>DEHE>[email protected]'5I8IBFJHDI=CIIJ8JFHIBJJI0IJGFFJGIIJJABH<)IFJJJIEDHHHHAFFFFFCC@    XT:A:R  NM:i:0  X0:i:2  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100    XA:Z:chr1,+13267477,100M,0;
chr1-33 0   chr1    48968233    37  100M    *   0   0   TAATAGTAGGCAATAAACAAAGAGAGCAACTTAGGAGCCAGATCACATGTGGCCGCTCGAGCAATATGGTAAAAGTTCTGGACTTCATTCTAGGTGAATG    1CCB=FFFHHHHHEDHJIIAFG4JIFJIJB)JJI?(&JJIJJEE)HIJJBJ?HJ(=B(I@?I?8DC8C>JHJH>@EDFDD5DDDDDDDDCFD:=DCC(DD    XT:A:U  NM:i:2  X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:0G53T45
chr1-32 0   chr1    88980623    37  100M    *   0   0   TAGTTCAGTAAACTATTTATCAAACAGGTGTCAGGTCATTTTAACATACTCCTTGCTTTGAACAATATTCATTCATACTTGGTACAAACTCTATATCCTA    B?CFDFFFHHFH3JIJJJIGJJJJJFJDEJGJ(EHFI>E=JIJ(GGJDFCH>>GJ=IHDJEHHDI>GEBJE@DD@HH'AA@ECC@BDEDDD@CDDADBDD    XT:A:U  NM:i:2  X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:32T44T22
chr1-31 16  chr1    227005594   37  100M    *   0   0   TCACCAGGCATCTTTACTGACTCACACCAATAGTAGTACTGGGATTAGAAATAAGACGCTGCAATACTCACAACCTAGGTGAAGTTAGTTAATTTGGGAA    D@D5B=DACDDDDDBEFECBFDC5BCDDDCDFIDC8ICEIJ=DHIGHIJIJJB0HJJCDJHJGJIJI9GGHGGJ3@IJJAIJGGBGJ7HFHHDEBFF@CC    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-30 0   chr1    9852129 37  100M    *   0   0   TGTGAAATGGAGTCAGCAGAGTGAGCCGGCCTCCACTCAGTGAGCCGGGTCTCCCCCACAGCCGGCATGTGCTGACCTCCTTCCAACTGCTCTACCAAGA    CBCDDFFDHGHHHIEJ+JD+?ECDDDDB    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-29 16  chr1    156397431   37  100M    *   0   0   TCAGCCTCCCGAGTAGCTGGGATTACAGGAACCTGCCACCACGCCCGGCTAATTTTTGTATTTTCAGTTGAGACGGGGTTTCACCATGTTGCCCAGGCTG    D1D(@9DDDC@D0C3=CDDJ;FDHDD@H2BDHIDAGDDDCDIFJ9GIFGIG@?)JJHJGFGJIB7JG>'IJIJJGJ+JJGIIHFIJIDHHHFFFFFFC@B    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:68A31
chr1-28 16  chr1    56986638    37  100M    *   0   0   ACTCAGAACAGGTCTCCTTGTGGAACCATGGCCTTCCTTTTGGATCCTGGCCATGAGAGCCCATTCTTAGGAACCATGTTTCAATTCCAGTAGGTGATGT    DD)DC@CJ@A)GIFJJJHHFFHFDDFFCCC    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-27 16  chr1    172015198   37  100M    *   0   0   AGGTGTCAGTCCTCCAGCTTTGTTCTTCTTTTATATTGTGTTGGCTATCCTGGGCTCTTTGCTTCTCCATACAAAACTTAGAATCAGTTTGTTGATATCC    B8BD>/D@CCEBBEBCH,F?CCD.E;HGJBJ)IGD7HED5@6JJJCHIGHJIJFDJCIJJHGJIJJJIEF:FEJHBJ.JJJIGHBHCF2DDFFCC@    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-26 0   chr1    233336763   37  100M    *   0   0   AGATATACAGCAAAGTTTGAAAGCTACAGTTCTGAGGACCATATTTATGGATTCCTTCTTATATGTTATCTGGGTTGATATAGAAATTCTTCCATGGCTA    CBCFDFF;HHDDHHB?C9DE?DCE@D?B&5E>DDD7DD?D    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:41G58
chr1-25 0   chr1    105787069   0   100M    *   0   0   GCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGGTGAGCATTTTTTCATGTGTTTTTTGGCTG    CCCDFFFFBGHHHHHCIGFJ:JAIGIJIJG)HCIIJGIHHJJJGEDHIHJHIII3J>JHJ?GDD?:;EFE(EDIJD?DDEAHCEDCDD?CDCF6D=>DDD    XT:A:R  NM:i:0  X0:i:52 XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-24 0   chr1    235841969   37  100M    *   0   0   GTTGGCTACTAGCTTAGCAGAGGTGCAAAACCATGAATTTCTGGTGGTATGGATTTTTTCAGCTATTTCAGATTCACCAGCAGGATCCAGCTGCTTGGGT    CCCFF?FFFHHHFGI,JEJIIG@IIBDJJIFDIEAIJB;JGADHJD,CBD@DEC;?DDHD@DCDEDDDAD?    XT:A:U  NM:i:2  X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:25G60T13
chr1-23 0   chr1    96545358    37  100M    *   0   0   AGTGAAAAAGGCTGGCTGCCCTTCAATATCATCTTCAAATGTTAACAACACTGAATATTAATAAATTTCCTTTAGCGAATAATGAATCCAGCCTTCCTTA    C@CF+FFFGGDHGJIBDJI2JGJIHHJJII?GJJJJGIJIJJGFJJG)IJ0HD0JIFJDJDFC;D7JGFFCEDFHADCDCCDEDDEAHDDD+9?<CA2:D    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-22 0   chr1    80270679    37  100M    *   0   0   TTGTACACCCTATTTCTGACCAGAAGAAGGAGCATTTTGCTTTTTGCCAAATGAGAAGTGCATTCTGGAAACACTTGATGCCTGCACCACACCTCGAGTT    ?@CFDDFFHFHHHJJJGC7J(GI8IJJJE?HHI>BJG*IJFJIDJHD0IEJIHDI>@H=EHGIAHJ33(EJCDEDA?FDG@DDBD    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-21 0   chr1    35923261    37  100M    *   0   0   CTAAGCAGCAGTGTTTTTGGATACTTTTTTTTTCTGTTTGTGAATAAGGCCAGCACTCAAGATGGGCAGCCAAGGGTGCACTGACTATTAGCTGGCCCAT    =@@DFDFEHGHHH8JIJGJH1JJHHJIHJGH?IIFEJIIG87JI=IAJJJBJIJD(IIFI8JIHF=JDHEJHEHDDCEDCDEACDDCCADXT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-20 16  chr1    112489190   37  100M    *   0   0   AGGGAATGAACTATGCACATCTATATAGTAACAGGGACAGATTTTTTTTTAACATGAGAGTGTAAAAAAAAGAAAAAGAAAAAAAAAGGCCAGGCACAGT    DACDABD@DDDDDA7DDDC8GHI@EI(DC?FG'+8.FBDJIHIEGG=IIG=I@*DFIJJIBIIJIJIIHJCHBGFJJJI@F>HJIIIHHAHFAFDFFC@1    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:33A66
chr1-19 0   chr1    160371244   37  100M    *   0   0   AGGCCCTGGGCACAGGCAGAGAGCCCACCGGCTGGTCATGAGGGCCTCTTCCTTTCTCTGACCCAGGCACCTCGAGGGCTCTTCTCCTGGGTTCCTTCCG    @@:FDDFFCHHAHI:GEJFJGF@JJJFIC9JIIJJJ?IIEFHGJ'G?BFFBIIDIG,J)AJIHEGFBHCI&ECCD@EDD?)DED(D>3C?ABEEDDD4BD    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:80A19
chr1-18 16  chr1    179855835   37  100M    *   0   0   AGCAATTAAAATAAATTAGGGTATCTTTAAAAGTTGTAAAATTATAGCAGTGAAGTACTGTTGACCAGGCACAGTGGCTCACACCTGTAATACCAGCACT    DCEDBBDD/DD9DDD@DDFB(DDDHCHDF;C?;FJGC/IJ8DHEJ:DFGGIGHBIGIJDI(JDHGJJGJIHJII@HJJJ3JIJDIJBBHHFHFDFFF@C@    XT:A:U  NM:i:2  X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:20T39C39
chr1-17 16  chr1    207455995   37  100M    *   0   0   GGTTCTTATGATTGGAAAGGTTAAAGAGTGACCTATAGGTCACTTTCCAATTATGAAAACAAAAAATTAAGAAATATATATATTTTCATTATTTCACTCC    CBDDDCDD:&DDCFCFDDHDEJEDCFDJ;;EHGCD;CG?DIHGGCIJJJJ-GIJ7GIFHHHCGI)JJJJIJEGJIGJJJIH@FDCC1    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-16 0   chr1    114154603   37  100M    *   0   0   TGTATCTTTCTGCTAAGCATAACAAGAAAGACAGAAAGCTCAACGGGAGGATTGAGGCTAGACTTAAAGTAGAGATCCCCTCAGAAACTGTGGAGTGAGG    CCCF8FFDHHHH4JIJIGIJIIFJHJJ?JEDI9BG?I>GHJ7FJJJIF67EIIHD2C>?>DDHDE8E7@JEJ(IFDDC;EDCC:FD>@DBC>D5D>=XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-15 16  chr1    169767580   37  100M    *   0   0   GGTGGGGGAGAGGAAAGGAAACGAGGGAGGAAAGGCCCTAATAGGGAGGATTTTGGAGTTTAGATTTTAAAATGATAAAGGTTGTTTGACACTCTAGGCA    DEDD9DDD@DD4DDDAEDDDC@D7=D;DA)7;IIJFD(J?JJDGI(IDGD7D'3JIE;H?AC@EHJJE?JJHDFJIIIECG)GGJJECHFHHFDFDFC@C    XT:A:U  NM:i:2  X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:45A35A18
chr1-14 0   chr1    117644126   37  100M    *   0   0   GCATTTCATTGTGGACTAATTTTCCCCCACTATTGAGGGAAGACCCTTTTGAGTACTCTATCTGATGCCCCATGAATGATAAAGTTTTATACTCTGGCTG    C?CFBDFFGHHHJI5CJ=CD9DC-HGIJDCJHHDBEDDCC&DDDBD39DBCDDDDDCD    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-13 0   chr1    104996994   37  100M    *   0   0   TTCTTGCTGGAACACATGTTTTCACCTTTACCTTCACCCACAGCCCAATGTGCATCAATATGGAGATAATGCAGTTCCATTTATACCTCTTTGTGGTTCA    =@?FFFDDHBHHHJHJIJ)JIJHBHIJ*G:CJCJJJI?G)>GJI;JD3FJ8FJFGD;DDDDFBED7C7&A(ABC9CD+DCC&DDCA    XT:A:U  NM:i:3  X0:i:1  X1:i:0  XM:i:3  XO:i:0  XG:i:0  MD:Z:18G63G12A4
chr1-12 16  chr1    108617705   37  100M    *   0   0   AGGTCGGGGAGATTGGGAAGAAGAATGAGCAAAGAAACCACCAGTGTGATCAGAGGAGGAAAGCAAAGCAGAGTCCTGTCCTGAAAACCAAATGAAGAAA    :=>+D(DCEC=@GHB(CDDDDHABDD+HBJJ9F?A35DDIE?JJHIHJJIEE?JFJ?7JBGJJI>JJGJBJIIBIJJJIIIIJGJGJHHDFHF3FFFCB@    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-11 16  chr1    72085324    37  100M    *   0   0   TACTAGCCTTGAAAATGTTTAAAATAATATTCCAGAGTTAATATTGTTGTCCCTGGTATGTTAAAGAGTATTTGTTATCATAGCCAATTCTTGAGTCTGC    8@DDCD4D>D?C3DF(DCCHDDDA;HDEIBFCHGHHHFFIFEG1JHIJIJCGEJIHJG)IH(IJ)BDJ??FHHJHCJJIFJHJJJGIGH)2HFFFA=HFG1JJFIIJJDJJIJDIGICHEFD@D3:0A/(BECDDDDCBE>BD8DDDDDC8C    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-8  0   chr1    79478960    37  100M    *   0   0   GGCAACACTTGAGAACACAAAGTGAGTTCTCACTTTGGGCGGTGGTTTCAGGCTTCAGGGTGGAGTTTTGTCAGGAACCCAACCTTTTCTGCCTAGAATT    @CCFDFDADHHAHFIH@ICJJHI5?JIJ)GCFEIJHG=II)HIGI9JJIJGHEJHFI8EIDG)GCI4FJF?I8HCDH;DD0&3CFDDDD@C4DCD6ADD>    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:81C18
chr1-7  0   chr1    178190761   37  100M    *   0   0   GTAGCCGGAATAAACAGTCACTGTGAGTTGTCCATTTTAGAGCATAGGTTTTCAGGTGGTGAAGACCTGTCCTTAGTTGAATTTGTATGTGAATTAAACT    B?<;FDDFHHHHHJEGJFCJJIFJJJA=JHHGIIGJJIIGIGJ(D:DAFG7)&DJID9J)FCD/HHJEDFIJ@D@DDADF?C@A@ADCDD@CDDD    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:52T47
chr1-6  0   chr1    42572411    37  100M    *   0   0   AACCCTTTATCAGGTATGTATTATAAACATCGACTCTGTGGCTTGCATTTTCATTCTCCTTATATATCTTTTGATGAATCAAAGTTTTTAATTTGAATAT    BCCFFFFDAH)HHJJHIGG,HFH2JIJJ4IDI93IJJ<=JJ>IH7IJIJBIBG)CFH7DHHFAHFHEDIFBEFH;EBICA?3DD5D(DDBACDC(BADD:    XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:94T5
chr1-5  0   chr1    153186635   37  100M    *   0   0   GTCTTGACTCTTTATCCACTTTGCCAGTCTGTGTCTTGTAATTGGGGCATTTAGCCTATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCT    C1@?FF=FHHHHHI?JJEJFIIIHG:.?>EEJEI(JG9J'IIHIJIHIJGJGJFJ9FJAG4EEC:DADE8DAEJFCCBBCDAEDDDD-DDDD@+DBC8D+    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
chr1-4  0   chr1    145038405   0   100M    *   0   0   AGTGGAAATAATACTCGTCAACATATGCCTTTCAAAAAAATTTTTTTTCATATTTTAAATTTACCTTTACTACCTATTTATTTGGTTCAAGGCTCCATTT    C:CFFFDDHFHDHJIIJJJJ29CJ+JJJIIJIIFIG?JI08?CJJIFIFDEFDGBD>JAIDJDJ>JCBG(CG=DE5?(EDB3HDD>ED2:CCHDBJA2CCHECDEFD,DDFBCHXT:A:U  NM:i:2  X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:92C5A1
chr1-2  0   chr1    62477842    37  100M    *   0   0   TAGGAAAATGGAGAAACTTTAATATGAAATCTTCCTGTTTTTCACATTATGTTTAGATTGTTACAGCATAAAATTTCAGAAACATTGCAAAAAGTTTTAA    @C=FFDFDHHHH>GJ@IEJGJIIJJJJF@JHHIIGGJICIAJFJIH)H7E?GHEDI>HHFAHC@)(D>DDDEDXT:A:U  NM:i:2  X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:77C0A21
chr1-1  0   chr1    11355150    37  100M    *   0   0   ATTTATTGGCTGTCTTTCAGGCACATTTTAGCTGTCATCCAACATTCTCAACCTTAGTCCCCTTCTCTGGGCTAAGGGGAGAATGATGGTCCTACCCCAG    BC?DFFFFHH7FJJJJJFDHID)JCH=3DIJ5JGDI8@@I@A=>3<:IDCA9DDFFI(FADEBDCDCCDDB(DC>    XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:100
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ cat G38L100c50Nhs20.
G38L100c50Nhs20.aln       G38L100c50Nhs20.sai       G38L100c50Nhs20.sam       G38L100c50Nhs20.snap.sam

(3) snap:

hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ cat G38L100c50Nhs20.snap.sam 
@HD VN:1.4  SO:unsorted
@RG ID:FASTQ    PL:Illumina PU:pu   LB:lb   SM:sm
@PG ID:SNAP PN:SNAP CL:single index G38L100c50Nhs20.fq -o G38L100c50Nhs20.snap.sam  VN:1.0beta.23
@SQ SN:chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38   LN:248956422
chr1-50 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  93465785    26  100M    *   0   0   TTCCACAATAGTTGAACTAATTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAA    @@CDFDFDHFHGHIJH:IJJJ(JJE?JDIDEJIB@FGJIGBHJ()HG8(CIICGFFHEH=GI3@&@DD58FADDACHDDHFCD8D,DCC<CEFD<EDDCD    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-48 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  228133746   70  100M    *   0   0   ATCATTGTATGCCACAGAAATAATTAAATTTCCTTGTCAACTGACACATTATTATTAGGCACTCTCACCAGATCTTTACCCATGGCCATTTAAAGTGTGG    @>CFFFFFH<<GC1IIDCFJJHIGIHJ(IID7IJ,FJJJHJJJJ)GGBHIJFJFIFIHFE=HEIEE;CA)G0(D()HC@D(:EFDDC@;DDAC95(D?BD    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-47 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  13772988    70  100M    *   0   0   TTCAGTAATTCAGAATAACACATGAGGGAATGAATGAATGAATAAATAAAAAAAAACTGAATGAATAAATTACAAAAAATTGTGTTTCAGGGAAGAAAAA    CC@F(FFFDFH.HDHIGI(JIIIGGIEEJIIIHJJHHH3IJJIIJ3=EI>JDIGH((IBJCIEHGD>;J@HF+DC)CCCADBDBD+BDDDD5B5DDDE(C    PG:Z:SNAP   NM:i:2  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-46 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  37474758    70  100M    *   0   0   GGGTCGGGGTCCTGTTCCCCGGTCCGCCGGGCCTCAGGACCCCTCCAACTTTGCCCAAGTTGGGAGAGCCGGGGAAGAGCACCAGGTTCCTGATCGGGAT    (5CBACDDD>FBDDDDDEC:CE(CBDFDDHEFH;FGEFHGHDGJJJDIGI:JEHJ=JJJJJH8CI?JJJG9JIII>IJIIGJ=EIJGAHHHHFFDFDCC?    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-45 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  29056657    70  100M    *   0   0   CTGGGATTACAGGTGCCCGCCACCATGCCCAGCTAATTTTTGTATTTTTGGTAGAGACAAGGTTTCACCATGTTGGCCGGGATTGTCTCGAACTCCTGAT    B@@FFFFFHHG)HIJJJJBJIJCJHGJIBFJJI3IIHDF@JIAJ9JJJIJJBIJJ?BJID8F:HFHA(+D>J>CG>7D=DDFF@EDC3D<CDDDC@BD@B    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-44 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  49993893    70  100M    *   0   0   CAATTTAGCCAAAACTGGCTAATCGTTTTACCAGAATCATTCCCATTGTTCAAGACCTATTTTAAGCTCCACTATCACCATAAAACTTTCCCGATCAGTT    C@CFFFFDHHHHH<IEJJ@JJJHI)IDIBIJA:HJHFJJJIJGGJJIIIIHGGJJGH<(IIIJI?ICDG;CDHFHCDCCB?FDDED:CD:>DD5C&DDCD    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-43 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  194714506   70  100M    *   0   0   AATATGTTTTAATAATATCATATTTAAATTTGATGATACTTTAAAAATGGTTCCATGTGTGTTCTCTTGGGTTATTTCACAATCAATAAAAGGTCTGCAA    CCCCDDC@E>CDCDDC>D9CD=C)CGC>E@7.HF)DIBJBJJ.JEJEJ@JJIIIIGD?<IHH)FJJIIH*DJIBIIJHJIHHJFHIGHHHHDFDFDFC@B    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-42 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  35706203    70  100M    *   0   0   CAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACGTGCCACCATGCCTGGCAATTTTTGTATTTTTAGTACAGATGGGG    CC@FDFFAHHGFHJIHJFJJII=@JEHIJIIJIJEJIJJHHGIJBBFJG6JJHJJG<F3JJHIFG(DCJDHDFDCHDDF7DDHBDFDDCDDCDCD;CBCB    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-41 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  156482338   70  100M    *   0   0   GTGTGTGCATAGGCAGGTCTGCGTGTACATGCAACGTGGGCACGTGTCCATGTGGATGCAGGCGGGGGTATATCCTGGTGCCTGTGTGTATGGGCCCACC    D;CCDDCDCDDDCD:EDA@<C<E(GDDDGDJDDHJ@CJJI,=FHJJIGJ7GEC?IGJJIFBBICHJEIJJHHAIJIJI.IJGJJGJJHHGHHFFFFFB=B    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-40 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  221779284   70  100M    *   0   0   CATGGCACATAGCACTTTGGTGATGGGGACTGCTTTGCTAATGTCAGGGTCAAGGGGTGCATGGACCATGGGCAGAGTGCTGGGCTCAGCCAAATGGTTC    DDBCDCDDDDDDD25F?DD@4I5HED?CAHGA?JJIIJB)IHFJJFCJII?@<HIIFGIJIJFG?JIJCIIJJ)IJJIJIJJIIEGJFHHHFFDFDFC@@    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-39 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  3895605 70  100M    *   0   0   GTCCTCTCCGGATTGACAGGAGTCAAAACATGAGATCGGCTTAGCTTCAGTTTCGTCATGGATTAACCACCTCCAAGGTGTCAACTCCAAAATGTCAAGA    DD5CCAD&8DAD>D&FDDDCDBDD?6DD.FHDDIFE?@IDEGIBCGD?JFJ>JGBI,IJIF.JJIHJJJEIEGFJ=JJHJHHJFHIJHHHHHFFAFFC@B  PG:Z:SNAP NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-38 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  33174926    70  100M    *   0   0   CACACATACATATATGTGTGTATATATATATATATATATATATACACACATATACATATATATGCACACACACATGTATGTATATGTATATGTATATGTG    CDDC(FBDC(AACBDDCBDDECEC5@H;HFDJFH>=FCHAHJFJ'H3JG9JFEHIJFDJJ9IJHEJIGJIJJJJJC;J?AJFJGEHFHDC>D?DDBDFB)DDDDDC5(9>F;G)FB84/AJE3JJIJIGIGJBBIGCJCJGJGHJIDJ>IB7IGJGEGCIIGFJJJEFHIIJHHF=HFF8=F??=    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-34 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  13267477    3   100M    *   0   0   ATACAGGGAAGGTTTTAATCTGTTTCAGACATTAGAAATACATATATTTATATATGGTATCTTTATTGGAGAACCTTTGGCCACATCAAAAGTATCAAAA    @CCFFFFFAHHHHDEIJJJFI)3DDI.DDH@EDEH>EHED>F>CD(DDDECDED?BC@D    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-33 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  48968233    70  100M    *   0   0   TAATAGTAGGCAATAAACAAAGAGAGCAACTTAGGAGCCAGATCACATGTGGCCGCTCGAGCAATATGGTAAAAGTTCTGGACTTCATTCTAGGTGAATG    1CCB=FFFHHHHHEDHJIIAFG4JIFJIJB)JJI?(&JJIJJEE)HIJJBJ?HJ(=B(I@?I?8DC8C>JHJH>@EDFDD5DDDDDDDDCFD:=DCC(DD    PG:Z:SNAP   NM:i:2  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-32 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  88980623    70  100M    *   0   0   TAGTTCAGTAAACTATTTATCAAACAGGTGTCAGGTCATTTTAACATACTCCTTGCTTTGAACAATATTCATTCATACTTGGTACAAACTCTATATCCTA    B?CFDFFFHHFH3JIJJJIGJJJJJFJDEJGJ(EHFI>E=JIJ(GGJDFCH>>GJ=IHDJEHHDI>GEBJE@DD@HH'AA@ECC@BDEDDD@CDDADBDD    PG:Z:SNAP   NM:i:2  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-31 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  227005594   70  100M    *   0   0   TCACCAGGCATCTTTACTGACTCACACCAATAGTAGTACTGGGATTAGAAATAAGACGCTGCAATACTCACAACCTAGGTGAAGTTAGTTAATTTGGGAA    D@D5B=DACDDDDDBEFECBFDC5BCDDDCDFIDC8ICEIJ=DHIGHIJIJJB0HJJCDJHJGJIJI9GGHGGJ3@IJJAIJGGBGJ7HFHHDEBFF@CC    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-11 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  72085324    70  100M    *   0   0   TACTAGCCTTGAAAATGTTTAAAATAATATTCCAGAGTTAATATTGTTGTCCCTGGTATGTTAAAGAGTATTTGTTATCATAGCCAATTCTTGAGTCTGC    8@DDCD4D>D?C3DF(DCCHDDDA;HDEIBFCHGHHHFFIFEG1JHIJIJCGEJIHJG)IH(IJ)BDJ??FHHJHCJJIFJHJJJGIGH)2HFFFA=HFG1JJFIIJJDJJIJDIGICHEFD@D3:0A/(BECDDDDCBE>BD8DDDDDC8C    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-8  0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  79478960    70  100M    *   0   0   GGCAACACTTGAGAACACAAAGTGAGTTCTCACTTTGGGCGGTGGTTTCAGGCTTCAGGGTGGAGTTTTGTCAGGAACCCAACCTTTTCTGCCTAGAATT    @CCFDFDADHHAHFIH@ICJJHI5?JIJ)GCFEIJHG=II)HIGI9JJIJGHEJHFI8EIDG)GCI4FJF?I8HCDH;DD0&3CFDDDD@C4DCD6ADD>    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-7  0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  178190761   70  100M    *   0   0   GTAGCCGGAATAAACAGTCACTGTGAGTTGTCCATTTTAGAGCATAGGTTTTCAGGTGGTGAAGACCTGTCCTTAGTTGAATTTGTATGTGAATTAAACT    B?<;FDDFHHHHHJEGJFCJJIFJJJA=JHHGIIGJJIIGIGJ(D:DAFG7)&DJID9J)FCD/HHJEDFIJ<FJAF@D@DDADF?C@A@ADCDD@CDDD    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-6  0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  42572411    70  100M    *   0   0   AACCCTTTATCAGGTATGTATTATAAACATCGACTCTGTGGCTTGCATTTTCATTCTCCTTATATATCTTTTGATGAATCAAAGTTTTTAATTTGAATAT    BCCFFFFDAH)HHJJHIGG,HFH2JIJJ4IDI93IJJ<=JJ>IH7IJIJBIBG)CFH7DHHFAHFHEDIFBEFH;EBICA?3DD5D(DDBACDC(BADD:    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-5  0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  153186635   70  100M    *   0   0   GTCTTGACTCTTTATCCACTTTGCCAGTCTGTGTCTTGTAATTGGGGCATTTAGCCTATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCT    C1@?FF=FHHHHHI?JJEJFIIIHG:.?>EEJEI(JG9J'IIHIJIHIJGJGJFJ9FJAG4EEC:DADE8DAEJFCCBBCDAEDDDD-DDDD@+DBC8D+    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-4  0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  145038405   3   100M    *   0   0   AGTGGAAATAATACTCGTCAACATATGCCTTTCAAAAAAATTTTTTTTCATATTTTAAATTTACCTTTACTACCTATTTATTTGGTTCAAGGCTCCATTT    C:CFFFDDHFHDHJIIJJJJ29CJ+JJJIIJIIFIG?JI08?CJJIFIFDEFDGBD>JAIDJDJ>JCBG(CG=DE5?(EDB3HDD>ED2:CCHDBJA2CCHECDEFD,DDFBCH<A7DCD-DDBDD(E    PG:Z:SNAP   NM:i:2  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-2  0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  62477842    70  100M    *   0   0   TAGGAAAATGGAGAAACTTTAATATGAAATCTTCCTGTTTTTCACATTATGTTTAGATTGTTACAGCATAAAATTTCAGAAACATTGCAAAAAGTTTTAA    @C=FFDFDHHHH>GJ@IEJGJIIJJJJF@JHHIIGGJ<IHJIG/J*?GD>ICIAJFJIH)H7E?GHEDI>HHFAHC@)(D>DDDED<DCDD=DBBC5DDE    PG:Z:SNAP   NM:i:2  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-1  0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  11355150    70  100M    *   0   0   ATTTATTGGCTGTCTTTCAGGCACATTTTAGCTGTCATCCAACATTCTCAACCTTAGTCCCCTTCTCTGGGCTAAGGGGAGAATGATGGTCCTACCCCAG    BC?DFFFFHH<FFJG(ICJIGJJIJJGIFJIJGJ(7FJJJJJFDHID)JCH=3DIJ5JGDI8@@I@A=>3<:IDCA9DDFFI(FADEBDCDCCDDB(DC>    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-30 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  9852129 70  100M    *   0   0   TGTGAAATGGAGTCAGCAGAGTGAGCCGGCCTCCACTCAGTGAGCCGGGTCTCCCCCACAGCCGGCATGTGCTGACCTCCTTCCAACTGCTCTACCAAGA    CBCDDFFDHGHHHIEJ+J<EFJIJIIJI><J(IIFJG)0JGIJ?8J5;J?D@9IJHDI=DI)DDHG@3FAI5FF?EDAHDC@DDGD3AA>D+?ECDDDDB  PG:Z:SNAP NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-29 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  156397431   68  100M    *   0   0   TCAGCCTCCCGAGTAGCTGGGATTACAGGAACCTGCCACCACGCCCGGCTAATTTTTGTATTTTCAGTTGAGACGGGGTTTCACCATGTTGCCCAGGCTG    D1D(@9DDDC@D0C3=CDDJ;FDHDD@H2BDHIDAGDDDCDIFJ9GIFGIG@?)JJHJGFGJIB7JG>'IJIJJGJ+JJGIIHFIJIDHHHFFFFFFC@B    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-28 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  56986638    70  100M    *   0   0   ACTCAGAACAGGTCTCCTTGTGGAACCATGGCCTTCCTTTTGGATCCTGGCCATGAGAGCCCATTCTTAGGAACCATGTTTCAATTCCAGTAGGTGATGT    DD)DC@CJ@A)GIFJJJHHFFHFDDFFCCC    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-27 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  172015198   70  100M    *   0   0   AGGTGTCAGTCCTCCAGCTTTGTTCTTCTTTTATATTGTGTTGGCTATCCTGGGCTCTTTGCTTCTCCATACAAAACTTAGAATCAGTTTGTTGATATCC    B8BD>/D;HHDDHHB?C9DE?DCE@D?B&5E>DDD7DD?D    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-25 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  196781488   0   100M    *   0   0   GCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGGTGAGCATTTTTTCATGTGTTTTTTGGCTG    CCCDFFFFBGHHHHHCIGFJ:JAIGIJIJG)HCIIJGIHHJJJGEDHIHJHIII3J>JHJ?GDD?:;EFE(EDIJD?DDEAHCEDCDD?CDCF6D=>DDD    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-24 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  235841969   70  100M    *   0   0   GTTGGCTACTAGCTTAGCAGAGGTGCAAAACCATGAATTTCTGGTGGTATGGATTTTTTCAGCTATTTCAGATTCACCAGCAGGATCCAGCTGCTTGGGT    CCCFF?FFFHHHFGI,JEJIIGBJG*IJFJIDJHD0IEJIHDI>@H=EHGIAHJ33(EJCDEDA?FDG+8.FBDJIHIEGG=IIG=I@*DFIJJIBIIJIJIIHJCHBGFJJJI@F>HJIIIHHAHFAFDFFC@1    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-19 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  160371244   70  100M    *   0   0   AGGCCCTGGGCACAGGCAGAGAGCCCACCGGCTGGTCATGAGGGCCTCTTCCTTTCTCTGACCCAGGCACCTCGAGGGCTCTTCTCCTGGGTTCCTTCCG    @@:FDDFFCHHAHI:GEJFJGF@JJJFIC9JIIJJJ?IIEFHGJ'G?BFFBIIDIG,J)AJIHEGFBHCI&ECCD@EDD?)DED(D>3C?ABEEDDD4BD    PG:Z:SNAP   NM:i:1  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-18 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  179855835   70  100M    *   0   0   AGCAATTAAAATAAATTAGGGTATCTTTAAAAGTTGTAAAATTATAGCAGTGAAGTACTGTTGACCAGGCACAGTGGCTCACACCTGTAATACCAGCACT    DCEDBBDD/DD9DDD@DDFB(DDDHCHDF;C?;FJGC/IJ8DHEJ:DFGGIGHBIGIJDI(JDHGJJGJIHJII@HJJJ3JIJDIJBBHHFHFDFFF@C@    PG:Z:SNAP   NM:i:2  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-17 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  207455995   70  100M    *   0   0   GGTTCTTATGATTGGAAAGGTTAAAGAGTGACCTATAGGTCACTTTCCAATTATGAAAACAAAAAATTAAGAAATATATATATTTTCATTATTTCACTCC    CBDDDCDD:&DDCFCFDDHDEJEDCFDJ;;EHGCD;CG?DIHGGCIJJJJ-GIJ7GIFHHHCGI)JJJJIJEGJIGJJJIHGHJ7FJJJIF67EIIHD2C>?>DDHDE8E7@JEJ(IFDDC;EDCC:FD>@DBC>D5D>=3JIE;H?AC@EHJJE?JJHDFJIIIECG)GGJJECHFHHFDFDFC@C    PG:Z:SNAP   NM:i:2  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-14 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  117644126   70  100M    *   0   0   GCATTTCATTGTGGACTAATTTTCCCCCACTATTGAGGGAAGACCCTTTTGAGTACTCTATCTGATGCCCCATGAATGATAAAGTTTTATACTCTGGCTG    C?CFBDFFGHHH<JAGCIJJIIIGJJI8:JIJC(JGGJBJH-GIJIJJ;IIH;>JI5CJ=CD9DC-HGIJDCJHHDBEDDCC&DDDBD39DBCDDDDDCD    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-13 0   chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  104996994   70  100M    *   0   0   TTCTTGCTGGAACACATGTTTTCACCTTTACCTTCACCCACAGCCCAATGTGCATCAATATGGAGATAATGCAGTTCCATTTATACCTCTTTGTGGTTCA    =@?FFFDDHBHHHJHJIJ)JIJ<IJII++>HBHIJ*G:CJCJJJI?G)>GJI;JD3FJ8FJFGD;DDDDFBED7C<?E@C>7&A(ABC9CD+DCC&DDCA    PG:Z:SNAP   NM:i:3  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
chr1-12 16  chr1__AC:CM000663.2__gi:568336023__LN:248956422__rl:Chromosome__M5:6aef897c3d6ff0c78aff06ac189178dd__AS:GRCh38  108617705   70  100M    *   0   0   AGGTCGGGGAGATTGGGAAGAAGAATGAGCAAAGAAACCACCAGTGTGATCAGAGGAGGAAAGCAAAGCAGAGTCCTGTCCTGAAAACCAAATGAAGAAA    :=>+D(DCEC=@GHB(CDDDDHABDD+HBJJ9F?A35DDIE?JJHIHJJIEE?JFJ?7JBGJJI>JJGJBJIIBIJJJIIIIJGJGJHHDFHF3FFFCB@    PG:Z:SNAP   NM:i:0  RG:Z:FASTQ  PL:Z:Illumina   PU:Z:pu LB:Z:lb SM:Z:sm
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$

(4)cs-bwamem：

+--------------------+---------+---------+----+--------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+
|              contig|    start|      end|mapq|readName|            sequence|                qual|cigar|basesTrimmedFromStart|basesTrimmedFromEnd|readPaired|properPair|readMapped|mateMapped|firstOfPair|secondOfPair|failedVendorQualityChecks|duplicateRead|readNegativeStrand|mateNegativeStrand|primaryAlignment|secondaryAlignment|supplementaryAlignment|mismatchingPositions|origQual|          attributes|recordGroupName|recordGroupSequencingCenter|recordGroupDescription|recordGroupRunDateEpoch|recordGroupFlowOrder|recordGroupKeySequence|recordGroupLibrary|recordGroupPredictedMedianInsertSize|recordGroupPlatform|recordGroupPlatformUnit|recordGroupSample|mateAlignmentStart|mateAlignmentEnd|mateContig|
+--------------------+---------+---------+----+--------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+
|[chr1,248956422,n...| 93465784| 93465884|  26| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|            true|             false|                 false|                 100|    null|NM:i:0    AS:i:100    X...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|101668921|101669021|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|231780491|231780591|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...| 69447775| 69447875|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...| 71519060| 71519160|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|187344346|187344446|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|188353053|188353153|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|242097330|242097430|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|112217125|112217225|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|218009808|218009908|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|147407851|147407951|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...| 45962351| 45962451|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...| 47126825| 47126925|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|152431792|152431892|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|237080611|237080711|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...| 82131491| 82131591|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...| 69486875| 69486975|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|224551051|224551151|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...|154119974|154120074|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,248956422,n...| 78244128| 78244228|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
+--------------------+---------+---------+----+--------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+
only showing top 20 rows

492条

(5):bwa-mem：

hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ cat G38L100c50Nhs20.bwamem.sam 
@SQ SN:chr1 LN:248956422
@PG ID:bwa  PN:bwa  VN:0.7.13-r1126 CL:bwa mem GRCH38BWAindex/GRCH38chr1L3556522.fasta fastq/g38L100c50Nhs20.fastq
chr1-50 0   chr1    93465785    26  100M    *   0   0   TTCCACAATAGTTGAACTAATTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAA    @@CDFDFDHFHGHIJH:IJJJ(JJE?JDIDEJIB@FGJIGBHJ()HG8(CIICGFFHEH=GI3@&@DD58FADDACHDDHFCD8D,DCCNM:i:0  MD:Z:100    AS:i:100    XS:i:90
chr1-48 0   chr1    228133746   60  100M    *   0   0   ATCATTGTATGCCACAGAAATAATTAAATTTCCTTGTCAACTGACACATTATTATTAGGCACTCTCACCAGATCTTTACCCATGGCCATTTAAAGTGTGG    @>CFFFFFH<@D(:EFDDC@;DDAC95(D?BD    NM:i:1  MD:Z:44G55  AS:i:95 XS:i:19
chr1-47 0   chr1    13772988    60  100M    *   0   0   TTCAGTAATTCAGAATAACACATGAGGGAATGAATGAATGAATAAATAAAAAAAAACTGAATGAATAAATTACAAAAAATTGTGTTTCAGGGAAGAAAAA    CC@F(FFFDFH.HDHIGI(JIIIGGIEEJIIIHJJHHH3IJJIIJ3=EI>JDIGH((IBJCIEHGD>;J@HF+DC)CCCADBDBD+BDDDD5B5DDDE(C    NM:i:2  MD:Z:56A15A27   AS:i:90 XS:i:23
chr1-46 16  chr1    37474758    60  100M    *   0   0   GGGTCGGGGTCCTGTTCCCCGGTCCGCCGGGCCTCAGGACCCCTCCAACTTTGCCCAAGTTGGGAGAGCCGGGGAAGAGCACCAGGTTCCTGATCGGGAT    (5CBACDDD>FBDDDDDEC:CE(CBDFDDHEFH;FGEFHGHDGJJJDIGI:JEHJ=JJJJJH8CI?JJJG9JIII>IJIIGJ=EIJGAHHHHFFDFDCC?    NM:i:1  MD:Z:22C77  AS:i:95 XS:i:0
chr1-45 0   chr1    29056657    60  100M    *   0   0   CTGGGATTACAGGTGCCCGCCACCATGCCCAGCTAATTTTTGTATTTTTGGTAGAGACAAGGTTTCACCATGTTGGCCGGGATTGTCTCGAACTCCTGAT    B@@FFFFFHHG)HIJJJJBJIJCJHGJIBFJJI3IIHDF@JIAJ9JJJIJJBIJJ?BJID8F:HFHA(+D>J>CG>7D=DDFF@EDC3D@BD@B    NM:i:0  MD:Z:100    AS:i:100    XS:i:64
chr1-44 0   chr1    49993893    60  100M    *   0   0   CAATTTAGCCAAAACTGGCTAATCGTTTTACCAGAATCATTCCCATTGTTCAAGACCTATTTTAAGCTCCACTATCACCATAAAACTTTCCCGATCAGTT    C@CFFFFDHHHHH@JJJHI)IDIBIJA:HJHFJJJIJGGJJIIIIHGGJJGH<(IIIJI?ICDG;CDHFHCDCCB?FDDED:CD:>DD5C&DDCD    NM:i:1  MD:Z:24C75  AS:i:95 XS:i:0
chr1-43 16  chr1    194714506   60  100M    *   0   0   AATATGTTTTAATAATATCATATTTAAATTTGATGATACTTTAAAAATGGTTCCATGTGTGTTCTCTTGGGTTATTTCACAATCAATAAAAGGTCTGCAA    CCCCDDC@E>CDCDDC>D9CD=C)CGC>E@7.HF)DIBJBJJ.JEJEJ@JJIIIIGD?@B    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-42 0   chr1    35706203    41  100M    *   0   0   CAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACGTGCCACCATGCCTGGCAATTTTTGTATTTTTAGTACAGATGGGG    CC@FDFFAHHGFHJIHJFJJII=@JEHIJIIJIJEJIJJHHGIJBBFJG6JJHJJGNM:i:0  MD:Z:100    AS:i:100    XS:i:84 XA:Z:chr1,-93072856,28M1D72M,3;
chr1-41 16  chr1    156482338   60  100M    *   0   0   GTGTGTGCATAGGCAGGTCTGCGTGTACATGCAACGTGGGCACGTGTCCATGTGGATGCAGGCGGGGGTATATCCTGGTGCCTGTGTGTATGGGCCCACC    D;CCDDCDCDDDCD:EDA@@CJJI,=FHJJIGJ7GEC?IGJJIFBBICHJEIJJHHAIJIJI.IJGJJGJJHHGHHFFFFFB=B    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-40 16  chr1    221779284   60  100M    *   0   0   CATGGCACATAGCACTTTGGTGATGGGGACTGCTTTGCTAATGTCAGGGTCAAGGGGTGCATGGACCATGGGCAGAGTGCTGGGCTCAGCCAAATGGTTC    DDBCDCDDDDDDD25F?DD@4I5HED?CAHGA?JJIIJB)IHFJJFCJII?@NM:i:1  MD:Z:39G60  AS:i:95 XS:i:0
chr1-39 16  chr1    3895605 60  100M    *   0   0   GTCCTCTCCGGATTGACAGGAGTCAAAACATGAGATCGGCTTAGCTTCAGTTTCGTCATGGATTAACCACCTCCAAGGTGTCAACTCCAAAATGTCAAGA    DD5CCAD&8DAD>D&FDDDCDBDD?6DD.FHDDIFE?@IDEGIBCGD?JFJ>JGBI,IJIF.JJIHJJJEIEGFJ=JJHJHHJFHIJHHHHHFFAFFC@B    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-38 16  chr1    33174926    60  100M    *   0   0   CACACATACATATATGTGTGTATATATATATATATATATATATACACACATATACATATATATGCACACACACATGTATGTATATGTATATGTATATGTG    CDDC(FBDC(AACBDDCBDDECEC5@H;HFDJFH>=FCHAHJFJ'H3JG9JFEHIJFDJJ9IJHEJIGJIJJJJJC;J?AJFJGEHFHDC>D?DDBDFB)DDDDDC5(9>F;G)FB84/AJE3JJIJIGIGJBBIGCJCJGJGHJIDJ>IB7IGJGEGCIIGFJJJEFHIIJHHF=HFF8=F??=    NM:i:1  MD:Z:14C85  AS:i:95 XS:i:32
chr1-34 16  chr1    12934213    0   100M    *   0   0   TTTTGATACTTTTGATGTGGCCAAAGGTTCTCCAATAAAGATACCATATATAAATATATGTATTTCTAATGTCTGAAACAGATTAAAACCTTCCCTGTAT    D@CB?DEDCEDDD(DC>F>DEHE>[email protected]'5I8IBFJHDI=CIIJ8JFHIBJJI0IJGFFJGIIJJABH<)IFJJJIEDHHHHAFFFFFCC@    NM:i:0  MD:Z:100    AS:i:100    XS:i:100    XA:Z:chr1,+13267477,100M,0;
chr1-33 0   chr1    48968233    60  100M    *   0   0   TAATAGTAGGCAATAAACAAAGAGAGCAACTTAGGAGCCAGATCACATGTGGCCGCTCGAGCAATATGGTAAAAGTTCTGGACTTCATTCTAGGTGAATG    1CCB=FFFHHHHHEDHJIIAFG4JIFJIJB)JJI?(&JJIJJEE)HIJJBJ?HJ(=B(I@?I?8DC8C>JHJH>@EDFDD5DDDDDDDDCFD:=DCC(DD    NM:i:2  MD:Z:0G53T45    AS:i:94 XS:i:0
chr1-32 0   chr1    88980623    60  100M    *   0   0   TAGTTCAGTAAACTATTTATCAAACAGGTGTCAGGTCATTTTAACATACTCCTTGCTTTGAACAATATTCATTCATACTTGGTACAAACTCTATATCCTA    B?CFDFFFHHFH3JIJJJIGJJJJJFJDEJGJ(EHFI>E=JIJ(GGJDFCH>>GJ=IHDJEHHDI>GEBJE@DD@HH'AA@ECC@BDEDDD@CDDADBDD    NM:i:2  MD:Z:32T44T22   AS:i:90 XS:i:0
chr1-31 16  chr1    227005594   60  100M    *   0   0   TCACCAGGCATCTTTACTGACTCACACCAATAGTAGTACTGGGATTAGAAATAAGACGCTGCAATACTCACAACCTAGGTGAAGTTAGTTAATTTGGGAA    D@D5B=DACDDDDDBEFECBFDC5BCDDDCDFIDC8ICEIJ=DHIGHIJIJJB0HJJCDJHJGJIJI9GGHGGJ3@IJJAIJGGBGJ7HFHHDEBFF@CC    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-30 0   chr1    9852129 60  100M    *   0   0   TGTGAAATGGAGTCAGCAGAGTGAGCCGGCCTCCACTCAGTGAGCCGGGTCTCCCCCACAGCCGGCATGTGCTGACCTCCTTCCAACTGCTCTACCAAGA    CBCDDFFDHGHHHIEJ+JD+?ECDDDDB    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-29 16  chr1    156397431   60  100M    *   0   0   TCAGCCTCCCGAGTAGCTGGGATTACAGGAACCTGCCACCACGCCCGGCTAATTTTTGTATTTTCAGTTGAGACGGGGTTTCACCATGTTGCCCAGGCTG    D1D(@9DDDC@D0C3=CDDJ;FDHDD@H2BDHIDAGDDDCDIFJ9GIFGIG@?)JJHJGFGJIB7JG>'IJIJJGJ+JJGIIHFIJIDHHHFFFFFFC@B    NM:i:1  MD:Z:68A31  AS:i:95 XS:i:55
chr1-28 16  chr1    56986638    51  100M    *   0   0   ACTCAGAACAGGTCTCCTTGTGGAACCATGGCCTTCCTTTTGGATCCTGGCCATGAGAGCCCATTCTTAGGAACCATGTTTCAATTCCAGTAGGTGATGT    DD)DC@CJ@A)GIFJJJHHFFHFDDFFCCC    NM:i:0  MD:Z:100    AS:i:100    XS:i:80
chr1-27 16  chr1    172015198   60  100M    *   0   0   AGGTGTCAGTCCTCCAGCTTTGTTCTTCTTTTATATTGTGTTGGCTATCCTGGGCTCTTTGCTTCTCCATACAAAACTTAGAATCAGTTTGTTGATATCC    B8BD>/D@CCEBBEBCH,F?CCD.E;HGJBJ)IGD7HED5@6JJJCHIGHJIJFDJCIJJHGJIJJJIEF:FEJHBJ.JJJIGHBHCF2DDFFCC@    NM:i:0  MD:Z:100    AS:i:100    XS:i:23
chr1-26 0   chr1    233336763   60  100M    *   0   0   AGATATACAGCAAAGTTTGAAAGCTACAGTTCTGAGGACCATATTTATGGATTCCTTCTTATATGTTATCTGGGTTGATATAGAAATTCTTCCATGGCTA    CBCFDFF;HHDDHHB?C9DE?DCE@D?B&5E>DDD7DD?D    NM:i:1  MD:Z:41G58  AS:i:95 XS:i:0
chr1-25 16  chr1    105822718   0   100M    *   0   0   CAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGC    DDD>=D6FCDC?DDCDECHAEDD?DJIDE(EFE;:?DDG?JHJ>J3IIIHJHIHDEGJJJHHIGJIICH)GJIJIGIAJ:JFGICHHHHHGBFFFFDCCC    NM:i:0  MD:Z:100    AS:i:100    XS:i:100
chr1-24 0   chr1    235841969   60  100M    *   0   0   GTTGGCTACTAGCTTAGCAGAGGTGCAAAACCATGAATTTCTGGTGGTATGGATTTTTTCAGCTATTTCAGATTCACCAGCAGGATCCAGCTGCTTGGGT    CCCFF?FFFHHHFGI,JEJIIG@IIBDJJIFDIEAIJB;JGADHJD,CBD@DEC;?DDHD@DCDEDDDAD?    NM:i:2  MD:Z:25G60T13   AS:i:90 XS:i:0
chr1-23 0   chr1    96545358    60  100M    *   0   0   AGTGAAAAAGGCTGGCTGCCCTTCAATATCATCTTCAAATGTTAACAACACTGAATATTAATAAATTTCCTTTAGCGAATAATGAATCCAGCCTTCCTTA    C@CF+FFFGGDHGJIBDJI2JGJIHHJJII?GJJJJGIJIJJGFJJG)IJ0HD0JIFJDJDFC;D7JGFFCEDFHADCDCCDEDDEAHDDD+9?<CA2:D    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-22 0   chr1    80270679    60  100M    *   0   0   TTGTACACCCTATTTCTGACCAGAAGAAGGAGCATTTTGCTTTTTGCCAAATGAGAAGTGCATTCTGGAAACACTTGATGCCTGCACCACACCTCGAGTT    ?@CFDDFFHFHHHJJJGC7J(GI8IJJJE?HHI>BJG*IJFJIDJHD0IEJIHDI>@H=EHGIAHJ33(EJCDEDA?FDG@DDBD    NM:i:0  MD:Z:100    AS:i:100    XS:i:19
chr1-21 0   chr1    35923261    60  100M    *   0   0   CTAAGCAGCAGTGTTTTTGGATACTTTTTTTTTCTGTTTGTGAATAAGGCCAGCACTCAAGATGGGCAGCCAAGGGTGCACTGACTATTAGCTGGCCCAT    =@@DFDFEHGHHH8JIJGJH1JJHHJIHJGH?IIFEJIIG87JI=IAJJJBJIJD(IIFI8JIHF=JDHEJHEHDDCEDCDEACDDCCADNM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-20 16  chr1    112489190   60  100M    *   0   0   AGGGAATGAACTATGCACATCTATATAGTAACAGGGACAGATTTTTTTTTAACATGAGAGTGTAAAAAAAAGAAAAAGAAAAAAAAAGGCCAGGCACAGT    DACDABD@DDDDDA7DDDC8GHI@EI(DC?FG'+8.FBDJIHIEGG=IIG=I@*DFIJJIBIIJIJIIHJCHBGFJJJI@F>HJIIIHHAHFAFDFFC@1    NM:i:1  MD:Z:33A66  AS:i:95 XS:i:28
chr1-19 0   chr1    160371244   60  100M    *   0   0   AGGCCCTGGGCACAGGCAGAGAGCCCACCGGCTGGTCATGAGGGCCTCTTCCTTTCTCTGACCCAGGCACCTCGAGGGCTCTTCTCCTGGGTTCCTTCCG    @@:FDDFFCHHAHI:GEJFJGF@JJJFIC9JIIJJJ?IIEFHGJ'G?BFFBIIDIG,J)AJIHEGFBHCI&ECCD@EDD?)DED(D>3C?ABEEDDD4BD    NM:i:1  MD:Z:80A19  AS:i:95 XS:i:0
chr1-18 16  chr1    179855835   60  100M    *   0   0   AGCAATTAAAATAAATTAGGGTATCTTTAAAAGTTGTAAAATTATAGCAGTGAAGTACTGTTGACCAGGCACAGTGGCTCACACCTGTAATACCAGCACT    DCEDBBDD/DD9DDD@DDFB(DDDHCHDF;C?;FJGC/IJ8DHEJ:DFGGIGHBIGIJDI(JDHGJJGJIHJII@HJJJ3JIJDIJBBHHFHFDFFF@C@    NM:i:2  MD:Z:20T39C39   AS:i:90 XS:i:34
chr1-17 16  chr1    207455995   60  100M    *   0   0   GGTTCTTATGATTGGAAAGGTTAAAGAGTGACCTATAGGTCACTTTCCAATTATGAAAACAAAAAATTAAGAAATATATATATTTTCATTATTTCACTCC    CBDDDCDD:&DDCFCFDDHDEJEDCFDJ;;EHGCD;CG?DIHGGCIJJJJ-GIJ7GIFHHHCGI)JJJJIJEGJIGJJJIH@FDCC1    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-16 0   chr1    114154603   60  100M    *   0   0   TGTATCTTTCTGCTAAGCATAACAAGAAAGACAGAAAGCTCAACGGGAGGATTGAGGCTAGACTTAAAGTAGAGATCCCCTCAGAAACTGTGGAGTGAGG    CCCF8FFDHHHH4JIJIGIJIIFJHJJ?JEDI9BG?I>GHJ7FJJJIF67EIIHD2C>?>DDHDE8E7@JEJ(IFDDC;EDCC:FD>@DBC>D5D>=NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-15 16  chr1    169767580   60  100M    *   0   0   GGTGGGGGAGAGGAAAGGAAACGAGGGAGGAAAGGCCCTAATAGGGAGGATTTTGGAGTTTAGATTTTAAAATGATAAAGGTTGTTTGACACTCTAGGCA    DEDD9DDD@DD4DDDAEDDDC@D7=D;DA)7;IIJFD(J?JJDGI(IDGD7D'3JIE;H?AC@EHJJE?JJHDFJIIIECG)GGJJECHFHHFDFDFC@C    NM:i:2  MD:Z:45A35A18   AS:i:90 XS:i:19
chr1-14 0   chr1    117644126   60  100M    *   0   0   GCATTTCATTGTGGACTAATTTTCCCCCACTATTGAGGGAAGACCCTTTTGAGTACTCTATCTGATGCCCCATGAATGATAAAGTTTTATACTCTGGCTG    C?CFBDFFGHHHJI5CJ=CD9DC-HGIJDCJHHDBEDDCC&DDDBD39DBCDDDDDCD    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-13 0   chr1    104996994   60  100M    *   0   0   TTCTTGCTGGAACACATGTTTTCACCTTTACCTTCACCCACAGCCCAATGTGCATCAATATGGAGATAATGCAGTTCCATTTATACCTCTTTGTGGTTCA    =@?FFFDDHBHHHJHJIJ)JIJHBHIJ*G:CJCJJJI?G)>GJI;JD3FJ8FJFGD;DDDDFBED7C7&A(ABC9CD+DCC&DDCA    NM:i:3  MD:Z:18G63G12A4 AS:i:85 XS:i:22
chr1-12 16  chr1    108617705   60  100M    *   0   0   AGGTCGGGGAGATTGGGAAGAAGAATGAGCAAAGAAACCACCAGTGTGATCAGAGGAGGAAAGCAAAGCAGAGTCCTGTCCTGAAAACCAAATGAAGAAA    :=>+D(DCEC=@GHB(CDDDDHABDD+HBJJ9F?A35DDIE?JJHIHJJIEE?JFJ?7JBGJJI>JJGJBJIIBIJJJIIIIJGJGJHHDFHF3FFFCB@    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
chr1-11 16  chr1    72085324    60  100M    *   0   0   TACTAGCCTTGAAAATGTTTAAAATAATATTCCAGAGTTAATATTGTTGTCCCTGGTATGTTAAAGAGTATTTGTTATCATAGCCAATTCTTGAGTCTGC    8@DDCD4D>D?C3DF(DCCHDDDA;HDEIBFCHGHHHFFIFEG1JHIJIJCGEJIHJG)IH(IJ)BDJ??FHHJHCJJIFJHJJJGIGH)2HFFFA=HFG1JJFIIJJDJJIJDIGICHEFD@D3:0A/(BECDDDDCBE>BD8DDDDDC8C    NM:i:0  MD:Z:100    AS:i:100    XS:i:38
chr1-8  0   chr1    79478960    60  100M    *   0   0   GGCAACACTTGAGAACACAAAGTGAGTTCTCACTTTGGGCGGTGGTTTCAGGCTTCAGGGTGGAGTTTTGTCAGGAACCCAACCTTTTCTGCCTAGAATT    @CCFDFDADHHAHFIH@ICJJHI5?JIJ)GCFEIJHG=II)HIGI9JJIJGHEJHFI8EIDG)GCI4FJF?I8HCDH;DD0&3CFDDDD@C4DCD6ADD>    NM:i:1  MD:Z:81C18  AS:i:95 XS:i:0
chr1-7  0   chr1    178190761   60  100M    *   0   0   GTAGCCGGAATAAACAGTCACTGTGAGTTGTCCATTTTAGAGCATAGGTTTTCAGGTGGTGAAGACCTGTCCTTAGTTGAATTTGTATGTGAATTAAACT    B?<;FDDFHHHHHJEGJFCJJIFJJJA=JHHGIIGJJIIGIGJ(D:DAFG7)&DJID9J)FCD/HHJEDFIJ@D@DDADF?C@A@ADCDD@CDDD    NM:i:1  MD:Z:52T47  AS:i:95 XS:i:0
chr1-6  0   chr1    42572411    60  100M    *   0   0   AACCCTTTATCAGGTATGTATTATAAACATCGACTCTGTGGCTTGCATTTTCATTCTCCTTATATATCTTTTGATGAATCAAAGTTTTTAATTTGAATAT    BCCFFFFDAH)HHJJHIGG,HFH2JIJJ4IDI93IJJ<=JJ>IH7IJIJBIBG)CFH7DHHFAHFHEDIFBEFH;EBICA?3DD5D(DDBACDC(BADD:    NM:i:1  MD:Z:94T5   AS:i:95 XS:i:19
chr1-5  0   chr1    153186635   46  100M    *   0   0   GTCTTGACTCTTTATCCACTTTGCCAGTCTGTGTCTTGTAATTGGGGCATTTAGCCTATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCT    C1@?FF=FHHHHHI?JJEJFIIIHG:.?>EEJEI(JG9J'IIHIJIHIJGJGJFJ9FJAG4EEC:DADE8DAEJFCCBBCDAEDDDD-DDDD@+DBC8D+    NM:i:0  MD:Z:100    AS:i:100    XS:i:82 XA:Z:chr1,-50361546,100M,4;
chr1-4  16  chr1    121241807   0   100M    *   0   0   AAATGGAGCCTTGAACCAAATAAATAGGTAGTAAAGGTAAATTTAAAATATGAAAAAAAATTTTTTTGAAAGGCATATGTTGACGAGTATTATTTCCACT    CCDDDDH3BDE(?5ED=GC(GBCJ>JDJDIAJ>DBGDFEDFIFIJJC?80IJ?GIFIIJIIJJJ+JC92JJJJIIJHDHFHDDFFFC:C    NM:i:0  MD:Z:100    AS:i:100    XS:i:100    XA:Z:chr1,+145038405,100M,0;chr1,-206260326,74M2D26M,2;chr1,-144029446,52M1I47M,1;
chr1-3  0   chr1    84685021    60  100M    *   0   0   TATTATTAAAACTATAAATGGACCAATTAAACAAACGTGTCATGAGCCAAGGAATATAAACTAATTCTTTACACCTGAAGTCCTTTAAAATGATTTAATT    CCCDFFB=HHHFHJIIJ:E@J>JA2CCHECDEFD,DDFBCHNM:i:2  MD:Z:92C5A1 AS:i:93 XS:i:20
chr1-2  0   chr1    62477842    60  100M    *   0   0   TAGGAAAATGGAGAAACTTTAATATGAAATCTTCCTGTTTTTCACATTATGTTTAGATTGTTACAGCATAAAATTTCAGAAACATTGCAAAAAGTTTTAA    @C=FFDFDHHHH>GJ@IEJGJIIJJJJF@JHHIIGGJICIAJFJIH)H7E?GHEDI>HHFAHC@)(D>DDDEDNM:i:2  MD:Z:77C0A21    AS:i:90 XS:i:0
chr1-1  0   chr1    11355150    60  100M    *   0   0   ATTTATTGGCTGTCTTTCAGGCACATTTTAGCTGTCATCCAACATTCTCAACCTTAGTCCCCTTCTCTGGGCTAAGGGGAGAATGATGGTCCTACCCCAG    BC?DFFFFHH7FJJJJJFDHID)JCH=3DIJ5JGDI8@@I@A=>3<:IDCA9DDFFI(FADEBDCDCCDDB(DC>    NM:i:0  MD:Z:100    AS:i:100    XS:i:0
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$

不知道有没有现成的可以直接比较与art的准确率。

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