BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524883.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 = 1,561,901 number of mapped reads = 1,444,510 (92.48%) number of supplementary alignments = 5,472 (0.35%) number of secondary alignments = 0 number of mapped bases = 84,509,124 bp number of sequenced bases = 84,484,117 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,915 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2623 >>>>>>> ACTG content number of A's = 20,535,140 bp (24.31%) number of C's = 14,864,348 bp (17.59%) number of T's = 27,965,095 bp (33.1%) number of G's = 21,108,905 bp (24.99%) number of N's = 10,629 bp (0.01%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 411,835 number of insertions = 4,940 mapped reads with insertion percentage = 0.34% number of deletions = 15,712 mapped reads with deletion percentage = 1.08% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.2763X There is a 2.48% of reference with a coverageData >= 1X There is a 0.18% 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 6755090 0.027101597472048024 0.5257824509837769 chr2 243199373 7155718 0.029423258422627593 0.2881495752064049 chr3 198022430 5612230 0.028341385367304097 0.18129491700435985 chr4 191154276 5338688 0.027928687297583653 0.19944660728097308 chr5 180915260 5114501 0.028270147029056586 0.18201561776302871 chr6 171115067 4868818 0.028453473357784444 0.19710274280267556 chr7 159138663 4700696 0.029538365544770222 0.3806126459105941 chr8 146364022 4359448 0.02978496997028409 0.2788007448090142 chr9 141213431 3525558 0.024966166284848643 0.23526489966652503 chr10 135534747 4050638 0.029886343462905494 0.25769927771131734 chr11 135006516 3902013 0.028902404977253097 0.2503885481552858 chr12 133851895 3766944 0.028142627341958812 0.1845639968489545 chr13 115169878 2712451 0.02355173980474304 0.165178774955668 chr14 107349540 2574147 0.02397911532736889 0.17602466175624398 chr15 102531392 2405469 0.023460805057635422 0.16534817910086813 chr16 90354753 2493153 0.027592936920540306 0.19296648208141676 chr17 81195210 2281249 0.028095856886138974 0.19393331949836923 chr18 78077248 2313807 0.02963484317480042 0.5023639919999419 chr19 59128983 1643198 0.027790060248457173 0.36480053531495543 chr20 63025520 1780222 0.028246050171422624 0.18343888405956196 chr21 48129895 1098813 0.022830155769091122 0.1809248609304788 chr22 51304566 1008771 0.019662401978022773 0.1500868628323191 chrMT 16571 9545 0.5760062760243799 0.9564476527475403 chrX 155270560 4781740 0.03079617926282999 0.21499197391055502 chrY 59373566 256217 0.004315337906434658 0.1238192034449051