BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173929.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,041,470 number of mapped reads = 1,991,496 (97.55%) number of supplementary alignments = 198,843 (9.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 996,160 number of mapped paired reads (second in pair) = 995,336 number of mapped paired reads (both in pair) = 1,959,178 number of mapped paired reads (singletons) = 32,318 number of mapped bases = 234,905,956 bp number of sequenced bases = 234,774,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,458,976 duplication rate = 61.54% >>>>>>> Insert size mean insert size = 1,109,832.5193 std insert size = 9,523,622.8585 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.9579 >>>>>>> ACTG content number of A's = 70,816,561 bp (30.16%) number of C's = 45,904,291 bp (19.55%) number of T's = 70,532,127 bp (30.04%) number of G's = 47,518,674 bp (20.24%) number of N's = 2,910 bp (0%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 2,420,109 number of insertions = 27,511 mapped reads with insertion percentage = 1.33% number of deletions = 53,427 mapped reads with deletion percentage = 2.62% homopolymer indels = 43.17% >>>>>>> Coverage mean coverageData = 0.0759X std coverageData = 1.2479X There is a 1.85% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 18816929 0.07549401050439108 0.9442287786758659 chr2 243199373 20814996 0.08558819763075623 3.3950651045222155 chr3 198022430 16529677 0.08347376102798051 0.7820870124793345 chr4 191154276 15819501 0.08275776682076419 0.9363822116182786 chr5 180915260 15351649 0.08485546769244341 0.7913088802716829 chr6 171115067 14277395 0.08343739245358213 0.8482356621913174 chr7 159138663 12974691 0.08153072770254455 0.8649836802124939 chr8 146364022 11245632 0.07683330811994221 0.9845149824886678 chr9 141213431 10184694 0.07212270056663378 0.8543951196773609 chr10 135534747 11308709 0.0834377106263385 1.0551851465122135 chr11 135006516 10331265 0.07652419532106139 0.7517980930551955 chr12 133851895 10905710 0.08147594772565603 0.7652822012028409 chr13 115169878 8053621 0.06992818903567824 0.7245944993610758 chr14 107349540 7568572 0.07050400029660117 0.7114980736817167 chr15 102531392 7210052 0.07032043415542433 0.7050122636282704 chr16 90354753 6557791 0.07257826270633488 0.805870280910624 chr17 81195210 6436090 0.0792668680824891 0.7564203997085559 chr18 78077248 6907880 0.08847494214960036 1.23765761607678 chr19 59128983 3961725 0.0670014060617278 0.7887107852340716 chr20 63025520 4923342 0.07811664227443106 0.7691162468676239 chr21 48129895 3329672 0.0691809529191784 0.7963193014061212 chr22 51304566 2896727 0.05646138786165738 0.6651412364605096 chrMT 16571 306001 18.466055156598877 16.268925493127675 chrX 155270560 5975010 0.038481280675486715 0.5271176411462183 chrY 59373566 2218625 0.0373672182667957 0.7021496534095446