BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231769.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,673,127 number of mapped reads = 1,062,642 (63.51%) number of supplementary alignments = 4,346 (0.26%) number of secondary alignments = 0 number of mapped bases = 66,799,553 bp number of sequenced bases = 66,770,350 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,369 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1583 >>>>>>> ACTG content number of A's = 18,719,885 bp (28.04%) number of C's = 10,764,063 bp (16.12%) number of T's = 21,448,032 bp (32.12%) number of G's = 15,835,950 bp (23.72%) number of N's = 2,420 bp (0%) GC percentage = 39.84% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 637,273 number of insertions = 5,110 mapped reads with insertion percentage = 0.48% number of deletions = 16,687 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 0.0216X std coverageData = 0.2108X There is a 1.98% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 5352996 0.02147635973191818 0.32737045467862813 chr2 243199373 4848676 0.019937041531764146 0.203571807715061 chr3 198022430 7184421 0.03628084454877157 0.20452921811984617 chr4 191154276 2750745 0.014390182932659062 0.13468615452529462 chr5 180915260 4208494 0.02326223890676773 0.1632586676840813 chr6 171115067 4461883 0.026075336779080943 0.1901390847770849 chr7 159138663 5561277 0.0349461086021566 0.2951635177500359 chr8 146364022 2599878 0.017763094813013542 0.37980866355420567 chr9 141213431 2396566 0.01697123271510909 0.15669414840564125 chr10 135534747 2390514 0.01763764682424943 0.17672200060625784 chr11 135006516 2203927 0.01632459725129119 0.15397893042067795 chr12 133851895 2245322 0.01677467472537464 0.13881238241444846 chr13 115169878 2719494 0.023612892947581312 0.16423752286494803 chr14 107349540 2910082 0.027108472006493925 0.18036761616724922 chr15 102531392 1155143 0.011266237368551478 0.11369469877577361 chr16 90354753 1017620 0.011262495510335799 0.12418488555201719 chr17 81195210 1624751 0.020010429186647832 0.1572160167366533 chr18 78077248 1331156 0.017049217718329415 0.2532467495276144 chr19 59128983 2091798 0.03537686416828783 0.2326779382572932 chr20 63025520 1658333 0.026312087548028162 0.17523426447699117 chr21 48129895 1469550 0.030532998253995774 0.19115337377671945 chr22 51304566 778559 0.015175238009030229 0.13208002566834778 chrMT 16571 74443 4.492366181884014 3.6778367860127417 chrX 155270560 3578324 0.023045733846776877 0.16847365575227202 chrY 59373566 185601 0.003125987076471034 0.07431016804419754