BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173953.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 = 18,210,678 number of mapped reads = 17,746,711 (97.45%) number of supplementary alignments = 2,404,712 (13.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,895,692 number of mapped paired reads (second in pair) = 8,851,019 number of mapped paired reads (both in pair) = 17,437,772 number of mapped paired reads (singletons) = 308,939 number of mapped bases = 2,003,643,487 bp number of sequenced bases = 2,002,202,796 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,298,114 duplication rate = 65.67% >>>>>>> Insert size mean insert size = 1,199,853.0229 std insert size = 10,248,883.1999 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.4607 >>>>>>> ACTG content number of A's = 592,322,978 bp (29.58%) number of C's = 401,952,488 bp (20.08%) number of T's = 588,046,494 bp (29.37%) number of G's = 419,865,974 bp (20.97%) number of N's = 14,862 bp (0%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 17,495,686 number of insertions = 216,988 mapped reads with insertion percentage = 1.18% number of deletions = 616,688 mapped reads with deletion percentage = 3.39% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 0.6472X std coverageData = 11.9826X There is a 13.07% of reference with a coverageData >= 1X There is a 10.17% of reference with a coverageData >= 2X There is a 7.79% of reference with a coverageData >= 3X There is a 6.32% of reference with a coverageData >= 4X There is a 4.81% of reference with a coverageData >= 5X There is a 3.95% of reference with a coverageData >= 6X There is a 3% of reference with a coverageData >= 7X There is a 2.55% of reference with a coverageData >= 8X There is a 1.94% of reference with a coverageData >= 9X There is a 1.71% of reference with a coverageData >= 10X There is a 1.3% of reference with a coverageData >= 11X There is a 1.17% of reference with a coverageData >= 12X There is a 0.88% of reference with a coverageData >= 13X There is a 0.8% of reference with a coverageData >= 14X There is a 0.6% of reference with a coverageData >= 15X There is a 0.55% of reference with a coverageData >= 16X There is a 0.42% of reference with a coverageData >= 17X There is a 0.38% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.13% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171069418 0.6863349720601097 4.938800986120108 chr2 243199373 182195080 0.7491593327421942 40.70338499315686 chr3 198022430 138591588 0.6998782309660577 2.5251936793966507 chr4 191154276 125591145 0.6570145728782965 4.457295135509899 chr5 180915260 122651678 0.6779509810283555 2.4771924595528216 chr6 171115067 117774394 0.6882760008503518 3.448013559807157 chr7 159138663 108954814 0.6846533202305464 4.46951427750002 chr8 146364022 99839897 0.6821341449608429 5.279223046155523 chr9 141213431 86366806 0.6116047559243851 4.654464037240746 chr10 135534747 96661404 0.7131854091999006 5.494768006281282 chr11 135006516 92419374 0.6845549143716886 2.740447598120264 chr12 133851895 91385474 0.6827357505846294 2.735743801405474 chr13 115169878 63942942 0.555205433142857 2.2539041437900864 chr14 107349540 62249978 0.5798811806738995 2.426683138153758 chr15 102531392 59500782 0.5803177040647219 2.5031554763382653 chr16 90354753 63590314 0.7037849353647173 3.57590572219695 chr17 81195210 60175270 0.741118472382792 3.163625284141089 chr18 78077248 53350019 0.6832978923642391 6.0022559989258895 chr19 59128983 41666175 0.704665848895118 3.8464825613582345 chr20 63025520 45658633 0.7244467479205249 2.9115727826305062 chr21 48129895 26901300 0.5589312006602134 3.581316113588339 chr22 51304566 27118039 0.5285696988451282 2.9060469948261045 chrMT 16571 2353359 142.01671594955042 98.14173240830715 chrX 155270560 49732830 0.32029787230753853 1.774880894797203 chrY 59373566 13902774 0.2341576384345855 3.5312509838077037