BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524833.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 = 875,207 number of mapped reads = 802,021 (91.64%) number of supplementary alignments = 3,366 (0.38%) number of secondary alignments = 0 number of mapped bases = 46,386,806 bp number of sequenced bases = 46,371,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,816 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1411 >>>>>>> ACTG content number of A's = 11,955,879 bp (25.78%) number of C's = 8,801,988 bp (18.98%) number of T's = 14,813,268 bp (31.94%) number of G's = 10,799,177 bp (23.29%) number of N's = 921 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 233,089 number of insertions = 3,514 mapped reads with insertion percentage = 0.44% number of deletions = 9,863 mapped reads with deletion percentage = 1.22% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 0.1714X There is a 1.41% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5257278 0.0210923366164853 0.2864655281172901 chr2 243199373 4086071 0.01680132209880327 0.2129388267126454 chr3 198022430 3144373 0.01587887291353813 0.13322667363447388 chr4 191154276 2128638 0.011135706951174872 0.11393098146634871 chr5 180915260 2205419 0.012190342594649009 0.11507602304909377 chr6 171115067 2976654 0.017395627703549917 0.14787090944226322 chr7 159138663 3644426 0.022900946453219856 0.2931005498780047 chr8 146364022 2357360 0.01610614389921589 0.15702547647567014 chr9 141213431 1598663 0.011320899072270258 0.12764037608949577 chr10 135534747 2597669 0.019166074069552067 0.1884912413852548 chr11 135006516 2231170 0.01652638751154796 0.14899950097291761 chr12 133851895 2158654 0.016127182958448217 0.13343360939942192 chr13 115169878 1080045 0.00937784270293314 0.10302829298300696 chr14 107349540 1418351 0.013212455311871853 0.12185624640720953 chr15 102531392 903549 0.008812413275341078 0.09908262835771574 chr16 90354753 1282663 0.01419585530824261 0.13183741613139702 chr17 81195210 849821 0.010466393276155084 0.10969605800424855 chr18 78077248 1031578 0.013212274080152006 0.20426786670317057 chr19 59128983 752234 0.012721916762884287 0.19798683067709874 chr20 63025520 803535 0.0127493593071505 0.11843038069073379 chr21 48129895 611041 0.012695664513708163 0.12009355445886258 chr22 51304566 520310 0.01014159246566865 0.10495788663963627 chrMT 16571 1340 0.08086416028000724 0.3028281817856311 chrX 155270560 2614598 0.016838980937532524 0.1425004799065246 chrY 59373566 131366 0.0022125334361759574 0.06890889423825566