BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524973.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 = 2,696,170 number of mapped reads = 2,483,574 (92.11%) number of supplementary alignments = 5,765 (0.21%) number of secondary alignments = 0 number of mapped bases = 143,628,520 bp number of sequenced bases = 143,585,373 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,473 duplication rate = 4.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6729 >>>>>>> ACTG content number of A's = 36,976,660 bp (25.75%) number of C's = 23,756,221 bp (16.55%) number of T's = 46,474,782 bp (32.37%) number of G's = 36,375,941 bp (25.33%) number of N's = 1,769 bp (0%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 688,353 number of insertions = 9,794 mapped reads with insertion percentage = 0.39% number of deletions = 25,338 mapped reads with deletion percentage = 1.01% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.0464X std coverageData = 0.4053X There is a 3.9% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11847135 0.04753101497789247 0.8073849064093666 chr2 243199373 12264647 0.05043042195672108 0.44165786318217504 chr3 198022430 10200683 0.05151276549833269 0.2663310033096051 chr4 191154276 8938386 0.04676006306026866 0.29079642290013535 chr5 180915260 9256534 0.05116502610117024 0.266053751811568 chr6 171115067 8142999 0.04758785501921932 0.35279693105022863 chr7 159138663 8077738 0.05075911690925793 0.5060310785029216 chr8 146364022 7380765 0.0504274540911427 0.4205259930924757 chr9 141213431 6128031 0.04339552517493892 0.32667738945888086 chr10 135534747 6870359 0.050690757551640986 0.39918571372164696 chr11 135006516 5787051 0.04286497549496055 0.3647419575291202 chr12 133851895 5433545 0.04059370993589594 0.2400085016554589 chr13 115169878 4609282 0.04002159314608287 0.2331819086616717 chr14 107349540 4561668 0.04249359615327648 0.2527026930294421 chr15 102531392 4126948 0.04025058003699004 0.25066235292998795 chr16 90354753 4066474 0.04500564569082492 0.2698667823127903 chr17 81195210 3739625 0.046057211995633736 0.2946373217491233 chr18 78077248 4156842 0.05324011932387781 0.6172962664292179 chr19 59128983 2909556 0.049206934609377605 0.5144845077815058 chr20 63025520 3048290 0.048365963501768805 0.2652131730637323 chr21 48129895 1917296 0.03983586500656193 0.2614687634161169 chr22 51304566 1597444 0.031136487929748786 0.20296914546000322 chrMT 16571 28386 1.712992577394243 1.8214143117305368 chrX 155270560 8108587 0.05222230795071519 0.3045940938979276 chrY 59373566 430249 0.007246473961156384 0.19908273147435743