BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524576.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 = 1,685,160 number of mapped reads = 1,526,227 (90.57%) number of supplementary alignments = 6,098 (0.36%) number of secondary alignments = 0 number of mapped bases = 88,727,136 bp number of sequenced bases = 88,700,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,591 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9132 >>>>>>> ACTG content number of A's = 22,529,817 bp (25.4%) number of C's = 17,448,881 bp (19.67%) number of T's = 27,633,074 bp (31.15%) number of G's = 21,087,278 bp (23.77%) number of N's = 1,356 bp (0%) GC percentage = 43.45% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 455,987 number of insertions = 5,054 mapped reads with insertion percentage = 0.33% number of deletions = 16,164 mapped reads with deletion percentage = 1.05% homopolymer indels = 44.4% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2718X There is a 2.55% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 8864778 0.035565720817201094 0.5081516250822603 chr2 243199373 7038499 0.028941271160267342 0.31291472493370903 chr3 198022430 4857681 0.024530963487318078 0.1742304608286142 chr4 191154276 5004150 0.026178593043872062 0.2011348097850489 chr5 180915260 4820613 0.026645695890993387 0.1807443266654726 chr6 171115067 3826676 0.022363173898649148 0.20201246034539405 chr7 159138663 4561368 0.028662852345315983 0.33496163134922013 chr8 146364022 7384680 0.05045420246787151 0.2968183907606918 chr9 141213431 3789570 0.02683576181928474 0.23111031103144317 chr10 135534747 4603614 0.03396630090732379 0.27399115005848795 chr11 135006516 3094084 0.022918034563605805 0.24905659213078557 chr12 133851895 4227460 0.03158311654833127 0.1964018908261603 chr13 115169878 1985434 0.01723917776486661 0.14401680387681273 chr14 107349540 2130236 0.019843922945547786 0.16041751939103313 chr15 102531392 2413954 0.023543560200567647 0.1690840006225167 chr16 90354753 2798942 0.03097725251930023 0.20528232526062773 chr17 81195210 3154112 0.03884603537573214 0.23122300412479718 chr18 78077248 2137680 0.02737903876939925 0.41448960649422495 chr19 59128983 1906614 0.032244999038796254 0.3399336502816292 chr20 63025520 2511342 0.03984643046181927 0.22091042857021623 chr21 48129895 1260464 0.026188795965584384 0.1925570092110474 chr22 51304566 762166 0.014855714791545065 0.1338024513820531 chrMT 16571 42590 2.5701526763623197 2.4096245491854624 chrX 155270560 5253999 0.03383770239509666 0.2271885758454404 chrY 59373566 296430 0.004992625842955095 0.14576182738433752