BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173943.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 = 4,246,646 number of mapped reads = 4,141,522 (97.52%) number of supplementary alignments = 517,523 (12.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,073,449 number of mapped paired reads (second in pair) = 2,068,073 number of mapped paired reads (both in pair) = 4,080,118 number of mapped paired reads (singletons) = 61,404 number of mapped bases = 471,024,481 bp number of sequenced bases = 470,691,858 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,276,632 duplication rate = 65.16% >>>>>>> Insert size mean insert size = 1,224,646.4788 std insert size = 10,543,518.7518 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.5865 >>>>>>> ACTG content number of A's = 141,991,026 bp (30.17%) number of C's = 92,181,948 bp (19.58%) number of T's = 140,804,283 bp (29.91%) number of G's = 95,710,832 bp (20.33%) number of N's = 3,769 bp (0%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 4,137,556 number of insertions = 50,881 mapped reads with insertion percentage = 1.19% number of deletions = 137,844 mapped reads with deletion percentage = 3.25% homopolymer indels = 41.36% >>>>>>> Coverage mean coverageData = 0.1522X std coverageData = 2.9635X There is a 3.31% of reference with a coverageData >= 1X There is a 2.51% of reference with a coverageData >= 2X There is a 1.87% of reference with a coverageData >= 3X There is a 1.5% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 0.92% of reference with a coverageData >= 6X There is a 0.68% of reference with a coverageData >= 7X There is a 0.58% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 37912863 0.15210739635429033 1.4524302027370923 chr2 243199373 44191399 0.18170852356597153 9.489235985242313 chr3 198022430 31648748 0.15982405629503688 1.1799682381230057 chr4 191154276 34206134 0.17894516782873326 1.5439945820960743 chr5 180915260 29351397 0.16223837060511093 1.1931466881004889 chr6 171115067 28973970 0.1693244815197951 1.324869204424392 chr7 159138663 24025143 0.1509698683342589 1.4999770046972642 chr8 146364022 23656831 0.16163009650008114 1.855046134231501 chr9 141213431 20045218 0.14194979796220658 1.4209427239031722 chr10 135534747 22688723 0.16740152250404097 1.7151820384938716 chr11 135006516 21908587 0.16227799701164053 1.2378294481032588 chr12 133851895 22350876 0.16698214097006248 1.2393950298172727 chr13 115169878 16668769 0.1447320192524646 1.1362559240529193 chr14 107349540 15089440 0.14056362048686935 1.120633515858857 chr15 102531392 13115816 0.12792000327080316 1.0610042880985282 chr16 90354753 13350236 0.14775355536636794 1.3195203365236403 chr17 81195210 11807774 0.14542451457419717 1.1793028792725615 chr18 78077248 13222485 0.1693513198620935 1.891610949075968 chr19 59128983 7788289 0.1317169449709629 1.1460423580779255 chr20 63025520 9378882 0.14881086264738475 1.1822839578164202 chr21 48129895 6625319 0.13765496475735092 1.468649313409463 chr22 51304566 5197903 0.10131462762982928 1.0597698324003924 chrMT 16571 681309 41.11453744493392 38.758520725935526 chrX 155270560 13342656 0.0859316537532936 0.8654545555006559 chrY 59373566 3795714 0.06392935873179657 1.078620351736802