BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525073.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 = 1,431,594 number of mapped reads = 1,322,336 (92.37%) number of supplementary alignments = 4,652 (0.32%) number of secondary alignments = 0 number of mapped bases = 77,250,558 bp number of sequenced bases = 77,226,774 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,313 duplication rate = 4.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8742 >>>>>>> ACTG content number of A's = 19,734,577 bp (25.55%) number of C's = 14,480,316 bp (18.75%) number of T's = 23,468,236 bp (30.39%) number of G's = 19,535,009 bp (25.3%) number of N's = 8,636 bp (0.01%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 360,603 number of insertions = 5,091 mapped reads with insertion percentage = 0.38% number of deletions = 14,574 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.1% >>>>>>> Coverage mean coverageData = 0.025X std coverageData = 0.2433X There is a 2.17% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.04% 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 6217397 0.02494435911555863 0.4243742093097536 chr2 243199373 6487651 0.026676265320799163 0.29797328673897383 chr3 198022430 5092468 0.025716622101849777 0.1794879926106573 chr4 191154276 4941386 0.02585025092506955 0.21609359463095335 chr5 180915260 4659992 0.025757871392385584 0.18062949894360233 chr6 171115067 4318541 0.025237643158565342 0.1869038140450349 chr7 159138663 4284304 0.026921829800719138 0.27719825909297885 chr8 146364022 3869005 0.026434126003998443 0.23678855594728399 chr9 141213431 3204285 0.022691078159555518 0.20704688327840262 chr10 135534747 3749754 0.02766636661814848 0.27328983404702184 chr11 135006516 3535491 0.02618755823607803 0.20670058607110947 chr12 133851895 3508733 0.02621354744361296 0.18555124406559034 chr13 115169878 2375660 0.02062744218588128 0.16106406850146768 chr14 107349540 2297361 0.02140075309125684 0.16569354182406418 chr15 102531392 2254301 0.02198644684351891 0.16687062426455512 chr16 90354753 2303535 0.025494342284351105 0.19158345563323387 chr17 81195210 2105499 0.025931320332812736 0.18831202860894355 chr18 78077248 2030528 0.02600665433289862 0.3104233073301436 chr19 59128983 1631966 0.027600102643402475 0.32118895821865506 chr20 63025520 1696510 0.02691782630274213 0.19165940257014755 chr21 48129895 1060989 0.02204428245688049 0.1931927542783221 chr22 51304566 964538 0.018800237000348077 0.15480280948300404 chrMT 16571 45706 2.7581920222074707 2.222501347909246 chrX 155270560 4337645 0.027936042737270992 0.20668170729610252 chrY 59373566 277313 0.004670647540354912 0.1698777209697454