BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716449.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 = 2,443,474 number of mapped reads = 2,238,372 (91.61%) number of supplementary alignments = 36,134 (1.48%) number of secondary alignments = 0 number of mapped bases = 175,598,469 bp number of sequenced bases = 175,525,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,306 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4853 >>>>>>> ACTG content number of A's = 42,674,539 bp (24.31%) number of C's = 33,853,696 bp (19.29%) number of T's = 54,802,962 bp (31.22%) number of G's = 44,184,839 bp (25.17%) number of N's = 9,952 bp (0.01%) GC percentage = 44.46% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,460,581 number of insertions = 16,145 mapped reads with insertion percentage = 0.71% number of deletions = 41,514 mapped reads with deletion percentage = 1.83% homopolymer indels = 44.89% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.5436X There is a 4.51% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 17406643 0.06983590624634793 0.7669604655247882 chr2 243199373 14247583 0.05858396271441045 1.0116784943083608 chr3 198022430 13916842 0.07027911939066701 0.33611143791299825 chr4 191154276 7283892 0.03810478191970971 0.26692714668544454 chr5 180915260 10988956 0.06074090156905504 0.30699208360291563 chr6 171115067 13320083 0.0778428412735858 0.41163917921447146 chr7 159138663 8444397 0.05306313903114795 0.7034146947870473 chr8 146364022 9434882 0.06446175686535861 0.6933422385535121 chr9 141213431 8620350 0.061044830785252996 0.4993998813792891 chr10 135534747 8768684 0.06469694446694176 0.471647250895725 chr11 135006516 7242962 0.05364898091289164 0.3795223645069676 chr12 133851895 6665371 0.049796612890687875 0.27699292099770684 chr13 115169878 5063804 0.04396812854138823 0.2512620006163655 chr14 107349540 3908514 0.03640922914061858 0.2794023614732701 chr15 102531392 3666455 0.035759340905076174 0.23810784547235606 chr16 90354753 4561087 0.050479768341572466 0.31433868539706494 chr17 81195210 6409815 0.07894326524926779 0.38522018020462484 chr18 78077248 5442361 0.06970482617420122 1.0703011636430921 chr19 59128983 3832067 0.06480860663542953 0.6556342694369688 chr20 63025520 3640305 0.05775922197865246 0.341348307857257 chr21 48129895 3644911 0.07573070749479092 0.35368342718001206 chr22 51304566 2719268 0.053002455960742365 0.2915007352912956 chrMT 16571 28759 1.735501780218454 1.653116230694342 chrX 155270560 5933414 0.0382133870065259 0.30869985203526007 chrY 59373566 407064 0.006855980319592055 0.19734570165602627