BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716208.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 = 3,769,057 number of mapped reads = 3,031,555 (80.43%) number of supplementary alignments = 71,130 (1.89%) number of secondary alignments = 0 number of mapped bases = 226,650,685 bp number of sequenced bases = 226,570,963 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,761 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2855 >>>>>>> ACTG content number of A's = 59,642,618 bp (26.32%) number of C's = 46,777,838 bp (20.65%) number of T's = 65,876,392 bp (29.08%) number of G's = 54,247,244 bp (23.94%) number of N's = 26,871 bp (0.01%) GC percentage = 44.59% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,657,940 number of insertions = 19,731 mapped reads with insertion percentage = 0.64% number of deletions = 46,913 mapped reads with deletion percentage = 1.53% homopolymer indels = 39.57% >>>>>>> Coverage mean coverageData = 0.0732X std coverageData = 0.5502X There is a 5.84% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18098182 0.07261037877213554 0.7087811866391851 chr2 243199373 19433832 0.07990905469974217 0.7920860301332348 chr3 198022430 15100148 0.07625473538527934 0.33187352367006634 chr4 191154276 14663694 0.076711305165886 0.37706107044479464 chr5 180915260 13810717 0.07633804356802185 0.3406564828084433 chr6 171115067 13056020 0.07629965162565142 0.3976346114983918 chr7 159138663 12286558 0.07720661823079411 0.7382267068985894 chr8 146364022 11590575 0.07919005532657472 0.7108858325279731 chr9 141213431 9550217 0.06762966477317586 0.600424512822906 chr10 135534747 10802883 0.07970563445254375 0.5730952119493617 chr11 135006516 10182250 0.0754204337811369 0.5977207845945113 chr12 133851895 10367803 0.07745727469902462 0.34444408692809986 chr13 115169878 7190900 0.06243733278939481 0.3004321234224455 chr14 107349540 6774074 0.06310296252783197 0.4067554826338772 chr15 102531392 6533805 0.06372492241205503 0.3071398886761478 chr16 90354753 6643193 0.07352344817986498 0.38584405554416307 chr17 81195210 6136806 0.07558088709912814 0.3840902498095392 chr18 78077248 6233025 0.07983151506569494 1.144609552455531 chr19 59128983 4534687 0.07669144250290928 0.5793739183858989 chr20 63025520 4783811 0.07590276129415513 0.357165066955309 chr21 48129895 2975307 0.0618182732374546 0.3388541279037889 chr22 51304566 2616887 0.05100690258251088 0.2732788561352523 chrMT 16571 23681 1.4290628205901876 1.7511370130407367 chrX 155270560 12695984 0.08176684620703371 0.47424604249829566 chrY 59373566 565646 0.009526899563351138 0.258412349584624