BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524594.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 = 1,840,227 number of mapped reads = 1,711,331 (93%) number of supplementary alignments = 3,869 (0.21%) number of secondary alignments = 0 number of mapped bases = 99,661,540 bp number of sequenced bases = 99,631,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,777 duplication rate = 3.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4202 >>>>>>> ACTG content number of A's = 24,702,486 bp (24.79%) number of C's = 18,255,499 bp (18.32%) number of T's = 32,250,004 bp (32.37%) number of G's = 24,422,694 bp (24.51%) number of N's = 627 bp (0%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 457,597 number of insertions = 6,818 mapped reads with insertion percentage = 0.4% number of deletions = 17,687 mapped reads with deletion percentage = 1.03% homopolymer indels = 44.27% >>>>>>> Coverage mean coverageData = 0.0322X std coverageData = 0.2804X There is a 2.8% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10135924 0.04066559176195593 0.4529345026670262 chr2 243199373 8841784 0.03635611346744714 0.3311552563738438 chr3 198022430 7036503 0.03553386856226338 0.21427155205243834 chr4 191154276 4520829 0.023650158890507894 0.20451632033203485 chr5 180915260 6279474 0.03470947669091043 0.21053447781269316 chr6 171115067 6406626 0.037440455199658135 0.2340318082815964 chr7 159138663 6166087 0.03874663066636421 0.39995955762796276 chr8 146364022 8421029 0.057534829153574364 0.37312315417380065 chr9 141213431 3493122 0.0247364714196343 0.24442815843056312 chr10 135534747 4252907 0.0313787209120625 0.2884277477478504 chr11 135006516 5091361 0.03771196495434339 0.2803312268358705 chr12 133851895 3375957 0.025221585394812677 0.1825702444501041 chr13 115169878 2412824 0.02095013072775852 0.1638181528822007 chr14 107349540 1820277 0.016956542151927247 0.15192736647705146 chr15 102531392 2463314 0.024024973736823937 0.1848485979422816 chr16 90354753 2857795 0.03162860729639757 0.21047586989053482 chr17 81195210 2168442 0.02670652616084126 0.1908619343835606 chr18 78077248 2689294 0.03444401626450768 0.40232875125543505 chr19 59128983 1969739 0.03331258039733239 0.3419943933983576 chr20 63025520 1860547 0.029520533904361282 0.19889997707331167 chr21 48129895 860710 0.01788306415378633 0.16604749245710754 chr22 51304566 1658303 0.03232271763101943 0.20096342375170628 chrMT 16571 10941 0.6602498340474323 1.0186104554704276 chrX 155270560 4609486 0.029686799609661998 0.22534065852196197 chrY 59373566 258265 0.00434983137108524 0.12487005860350409