BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525203.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 = 2,326,977 number of mapped reads = 2,157,695 (92.73%) number of supplementary alignments = 7,639 (0.33%) number of secondary alignments = 0 number of mapped bases = 126,477,987 bp number of sequenced bases = 126,434,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,127 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1134 >>>>>>> ACTG content number of A's = 31,642,208 bp (25.03%) number of C's = 24,672,394 bp (19.51%) number of T's = 39,485,034 bp (31.23%) number of G's = 30,632,398 bp (24.23%) number of N's = 2,916 bp (0%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 644,245 number of insertions = 8,906 mapped reads with insertion percentage = 0.41% number of deletions = 26,804 mapped reads with deletion percentage = 1.23% homopolymer indels = 42.57% >>>>>>> Coverage mean coverageData = 0.0409X std coverageData = 0.3803X There is a 3.6% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 14306723 0.057398946259796885 0.7077680872273218 chr2 243199373 10145158 0.041715395376451074 0.4945379541428393 chr3 198022430 7629602 0.03852897876265835 0.21919798164416776 chr4 191154276 6906387 0.03612991110907715 0.2322539343688458 chr5 180915260 5593949 0.030920271733849317 0.19569380368303527 chr6 171115067 7533663 0.044026882799280326 0.2629025510194035 chr7 159138663 9042720 0.05682289790256689 0.6773161858194803 chr8 146364022 8194438 0.05598669596548802 0.38400490029716683 chr9 141213431 4131464 0.02925687713090124 0.25957550109321975 chr10 135534747 8304558 0.06127253847310461 0.39485777172514935 chr11 135006516 5602745 0.041499811757234 0.298708139807371 chr12 133851895 5529716 0.04131219808281385 0.22782157055896687 chr13 115169878 3770633 0.03273974988494822 0.20212121349811057 chr14 107349540 2830035 0.02636280509446058 0.18964341029804424 chr15 102531392 3425859 0.03341278152158512 0.2073998923453477 chr16 90354753 3307378 0.03660436103455454 0.24388674972514815 chr17 81195210 2207849 0.02719186267268722 0.19294118680187355 chr18 78077248 2655616 0.03401267421720602 0.5512770595989994 chr19 59128983 2504769 0.04236110402913576 0.5041083127041041 chr20 63025520 2317010 0.0367630445571889 0.21802451472427792 chr21 48129895 1766019 0.036692766522760954 0.2367319622707591 chr22 51304566 1444073 0.028147065896629943 0.18480460758148815 chrMT 16571 40797 2.4619516021966086 2.1129560348225085 chrX 155270560 6885758 0.04434683561391161 0.25577911434242023 chrY 59373566 401068 0.006754992617421699 0.19322811899534623