BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695979.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 13,021,589 number of mapped reads = 11,492,920 (88.26%) number of supplementary alignments = 16,069 (0.12%) number of secondary alignments = 0 number of mapped bases = 1,560,830,627 bp number of sequenced bases = 1,549,763,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,529,788 duplication rate = 18.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.1575 >>>>>>> ACTG content number of A's = 426,219,648 bp (27.5%) number of C's = 344,817,883 bp (22.25%) number of T's = 426,641,274 bp (27.53%) number of G's = 352,084,240 bp (22.72%) number of N's = 0 bp (0%) GC percentage = 44.97% >>>>>>> Mismatches and indels general error rate = 0.0208 number of mismatches = 21,893,212 number of insertions = 9,527,862 mapped reads with insertion percentage = 49.07% number of deletions = 9,951,589 mapped reads with deletion percentage = 51.73% homopolymer indels = 36.7% >>>>>>> Coverage mean coverageData = 0.5042X std coverageData = 1.7385X There is a 17.7% of reference with a coverageData >= 1X There is a 10.06% of reference with a coverageData >= 2X There is a 6.26% of reference with a coverageData >= 3X There is a 4.14% of reference with a coverageData >= 4X There is a 2.86% of reference with a coverageData >= 5X There is a 2.04% of reference with a coverageData >= 6X There is a 1.49% of reference with a coverageData >= 7X There is a 1.12% of reference with a coverageData >= 8X There is a 0.85% of reference with a coverageData >= 9X There is a 0.66% of reference with a coverageData >= 10X There is a 0.51% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 178321939 0.7154322756933071 2.3033833999848503 chr2 243199373 122339219 0.5030408487113986 1.7424088137447569 chr3 198022430 103414654 0.5222370718307012 1.636985484708525 chr4 191154276 53285019 0.2787539997274244 1.178108884133571 chr5 180915260 123240601 0.6812062232892903 2.091798392216823 chr6 171115067 73924536 0.4320165213738893 1.46176090418813 chr7 159138663 92474542 0.5810941241852711 1.7806798145377527 chr8 146364022 68668798 0.4691644644747464 1.5690588728379986 chr9 141213431 65794535 0.46592264300978564 1.659655303668913 chr10 135534747 68607655 0.506199749647963 1.6246641247213416 chr11 135006516 87417370 0.6475048211747054 1.9153193687929224 chr12 133851895 76364330 0.5705136262732776 1.7792907571058219 chr13 115169878 28127023 0.2442220438924143 0.9999816778977585 chr14 107349540 35226608 0.32814866277023635 1.2318800227017754 chr15 102531392 60367932 0.5887751138695162 1.9112937554639504 chr16 90354753 67034908 0.7419079326131299 2.3432621199098076 chr17 81195210 48960458 0.6029968762935646 1.8609745533131063 chr18 78077248 28822359 0.369151830248935 1.4488777083482065 chr19 59128983 24838494 0.4200730798972139 1.52052319545108 chr20 63025520 55805464 0.8854423414515263 2.5478308812253605 chr21 48129895 14120819 0.29338977365315255 1.8919900008681787 chr22 51304566 20997295 0.40926756889435534 1.4635240251032182 chrMT 16571 248571 15.000362078329612 15.787992305330897 chrX 155270560 60662685 0.3906901926546797 1.3546560767570994 chrY 59373566 1764813 0.02972388419452522 0.578310506840322