BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525218.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,820,537 number of mapped reads = 1,406,159 (77.24%) number of supplementary alignments = 4,353 (0.24%) number of secondary alignments = 0 number of mapped bases = 83,015,407 bp number of sequenced bases = 82,988,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,767 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8924 >>>>>>> ACTG content number of A's = 20,827,005 bp (25.1%) number of C's = 17,094,741 bp (20.6%) number of T's = 26,291,352 bp (31.68%) number of G's = 18,773,095 bp (22.62%) number of N's = 2,027 bp (0%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 417,089 number of insertions = 7,411 mapped reads with insertion percentage = 0.52% number of deletions = 17,062 mapped reads with deletion percentage = 1.2% homopolymer indels = 42.4% >>>>>>> Coverage mean coverageData = 0.0268X std coverageData = 0.2619X There is a 2.45% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8635940 0.03464761678567693 0.4678700926991679 chr2 243199373 6559246 0.026970653415294785 0.32062338680460767 chr3 198022430 7668859 0.03872722398164693 0.21335842276011283 chr4 191154276 4524200 0.02366779386091264 0.17355824418679153 chr5 180915260 3611859 0.01996436895373005 0.1514480191550051 chr6 171115067 5133934 0.030002816759555136 0.20658486550448205 chr7 159138663 5983927 0.03760196854236484 0.45557130329560735 chr8 146364022 4698978 0.032104734044545453 0.24530646394133326 chr9 141213431 2700671 0.019124746002382734 0.18564424298058918 chr10 135534747 4323295 0.03189805637074012 0.278263200693191 chr11 135006516 3697788 0.027389700212691957 0.20661017399100018 chr12 133851895 3320425 0.02480670893751635 0.1712888682349946 chr13 115169878 2541074 0.02206370314988091 0.16091871900371807 chr14 107349540 3044053 0.028356460586603353 0.18696100744965755 chr15 102531392 2250194 0.021946390818530972 0.16099688706524953 chr16 90354753 2261002 0.02502360888530125 0.1836748818139245 chr17 81195210 1962398 0.024168888780508112 0.1712949519221524 chr18 78077248 1742392 0.022316257868105187 0.33451174184225524 chr19 59128983 1477425 0.024986477443726708 0.3267182187575672 chr20 63025520 1520109 0.024118944199111723 0.16821842131266376 chr21 48129895 1068638 0.022203206551769956 0.17038720325381837 chr22 51304566 730520 0.014238888601065255 0.1280324528474013 chrMT 16571 62733 3.785709975257981 2.8242214690333647 chrX 155270560 3263747 0.02101974128257153 0.16925931540597255 chrY 59373566 232000 0.003907462792448748 0.1164537299560873