BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230361.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 = 299,676 number of mapped reads = 262,981 (87.76%) number of supplementary alignments = 2,182 (0.73%) number of secondary alignments = 0 number of mapped bases = 17,596,338 bp number of sequenced bases = 17,587,300 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,592 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9884 >>>>>>> ACTG content number of A's = 5,104,287 bp (29.02%) number of C's = 3,181,563 bp (18.09%) number of T's = 5,634,746 bp (32.04%) number of G's = 3,658,125 bp (20.8%) number of N's = 8,579 bp (0.05%) GC percentage = 38.89% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 157,936 number of insertions = 1,523 mapped reads with insertion percentage = 0.58% number of deletions = 5,368 mapped reads with deletion percentage = 2.02% homopolymer indels = 46.7% >>>>>>> Coverage mean coverageData = 0.0057X std coverageData = 0.0869X There is a 0.54% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 1588570 0.006373384321477779 0.1032386221568617 chr2 243199373 1263467 0.005195190203060269 0.08416319976459893 chr3 198022430 1457049 0.007357999798305676 0.08984421722813558 chr4 191154276 1518136 0.007941941094741715 0.09394051398126467 chr5 180915260 1112975 0.006151913332241846 0.0816697206634391 chr6 171115067 883710 0.005164419565694937 0.078249269022904 chr7 159138663 801439 0.005036104896771691 0.09069849241165016 chr8 146364022 996523 0.006808524297043436 0.1153855147890716 chr9 141213431 969003 0.006861974764992432 0.09460634985362044 chr10 135534747 665008 0.004906549904874209 0.08794984302331366 chr11 135006516 724842 0.0053689408591211995 0.08366100844077777 chr12 133851895 839817 0.0062742257029681945 0.08264618928959733 chr13 115169878 602004 0.005227095925203637 0.07540314531141103 chr14 107349540 594710 0.005539939901000042 0.07839187109232933 chr15 102531392 502020 0.004896256553310034 0.0727221944144971 chr16 90354753 338608 0.003747539434920485 0.0671642490046075 chr17 81195210 357464 0.004402525715494794 0.06957004551943974 chr18 78077248 512200 0.006560169743687687 0.12314998960835623 chr19 59128983 201789 0.00341269187734888 0.07178127592748294 chr20 63025520 353554 0.0056096958819221165 0.07838700436082822 chr21 48129895 212916 0.004423778609947102 0.06953895984760067 chr22 51304566 186453 0.0036342379350796966 0.06259143210341053 chrMT 16571 1089 0.06571721682457304 0.26359984875831366 chrX 155270560 867350 0.005586055721058776 0.07875471731196573 chrY 59373566 45642 7.687259343661454E-4 0.033635215964564966