BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525260.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 = 968,341 number of mapped reads = 885,809 (91.48%) number of supplementary alignments = 3,311 (0.34%) number of secondary alignments = 0 number of mapped bases = 51,237,463 bp number of sequenced bases = 51,220,572 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,890 duplication rate = 1.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9084 >>>>>>> ACTG content number of A's = 13,247,226 bp (25.86%) number of C's = 9,653,502 bp (18.85%) number of T's = 16,442,168 bp (32.1%) number of G's = 11,876,578 bp (23.19%) number of N's = 1,098 bp (0%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 257,553 number of insertions = 4,280 mapped reads with insertion percentage = 0.48% number of deletions = 10,705 mapped reads with deletion percentage = 1.2% homopolymer indels = 42.87% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.189X There is a 1.55% of reference with a coverageData >= 1X There is a 0.07% 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 5421216 0.02175006015331051 0.32672368613975955 chr2 243199373 4107271 0.016888493376173302 0.2225406592355369 chr3 198022430 3641605 0.018389861188957232 0.14363717185068398 chr4 191154276 2892222 0.015130302395118799 0.13118381070363125 chr5 180915260 2364838 0.013071523098714835 0.1203751915028377 chr6 171115067 3103150 0.018134872950726192 0.15066483806186426 chr7 159138663 3677104 0.0231062893873879 0.3161411805000027 chr8 146364022 3405917 0.02327017906080772 0.20208477204885172 chr9 141213431 1626402 0.011517332228830274 0.13568042434538252 chr10 135534747 3328234 0.02455631543695581 0.21715405946932903 chr11 135006516 2207029 0.016347573920061753 0.15357980471028582 chr12 133851895 2249472 0.016805679142607582 0.13720389474615058 chr13 115169878 1545868 0.013422502713773822 0.12134469803664984 chr14 107349540 1099358 0.010240919523269498 0.10740668206309731 chr15 102531392 1334786 0.013018315405295581 0.12086560149388906 chr16 90354753 1269889 0.014054479236969416 0.13614658524819898 chr17 81195210 854720 0.010526729347704131 0.10979421435531968 chr18 78077248 1100947 0.01410074033347077 0.2417890888921248 chr19 59128983 925525 0.015652645336382668 0.24922856290271717 chr20 63025520 880315 0.013967595983341352 0.124798742739854 chr21 48129895 696989 0.014481415344870376 0.12736630938752802 chr22 51304566 501620 0.009777297404679341 0.10363880172544453 chrMT 16571 5282 0.3187496228350733 0.6316900466362593 chrX 155270560 2858413 0.01840923997440339 0.14993499255529977 chrY 59373566 139291 0.0023460103440645624 0.06866060959776574