BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717036.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 = 1,837,125 number of mapped reads = 1,665,470 (90.66%) number of supplementary alignments = 44,880 (2.44%) number of secondary alignments = 0 number of mapped bases = 127,002,084 bp number of sequenced bases = 126,953,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,761 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5422 >>>>>>> ACTG content number of A's = 33,849,793 bp (26.66%) number of C's = 25,367,205 bp (19.98%) number of T's = 37,774,020 bp (29.75%) number of G's = 29,946,790 bp (23.59%) number of N's = 15,491 bp (0.01%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 975,544 number of insertions = 11,345 mapped reads with insertion percentage = 0.67% number of deletions = 28,077 mapped reads with deletion percentage = 1.66% homopolymer indels = 39.86% >>>>>>> Coverage mean coverageData = 0.041X std coverageData = 0.3609X There is a 3.61% of reference with a coverageData >= 1X There is a 0.35% 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 10969997 0.04401191441765756 0.5365521423547246 chr2 243199373 11185679 0.045993864466089725 0.5358497300440103 chr3 198022430 9703295 0.04900098943336874 0.25113849624615625 chr4 191154276 5258785 0.027510684615812624 0.1957604496016221 chr5 180915260 8175060 0.045187232961995574 0.23811444065288795 chr6 171115067 9336101 0.054560367848846415 0.297820163694106 chr7 159138663 6432775 0.04042245221074906 0.5191734740247148 chr8 146364022 9157156 0.06256425503256531 0.47850036822039643 chr9 141213431 5599519 0.03965287834412861 0.33751431709729296 chr10 135534747 6023624 0.04444339280760232 0.3464162285914428 chr11 135006516 5083336 0.03765252337894565 0.29979164882272896 chr12 133851895 4666950 0.03486652168801943 0.20711562770351322 chr13 115169878 4511367 0.0391714142477428 0.21771299200684174 chr14 107349540 2995045 0.027899933246104267 0.20788615453118062 chr15 102531392 2742139 0.02674438478315012 0.17898477324600204 chr16 90354753 3101332 0.03432394973178666 0.2385070398061223 chr17 81195210 3593810 0.04426135482622682 0.26167492079767596 chr18 78077248 3875640 0.049638532341713684 0.655844913554413 chr19 59128983 2158754 0.036509236088163394 0.4249866645533408 chr20 63025520 2351105 0.0373040158970525 0.24919720572853918 chr21 48129895 2869507 0.05962005526918353 0.2825718141292944 chr22 51304566 1777848 0.034652822128930984 0.20884815550431277 chrMT 16571 3980 0.24017862530927525 1.2741794404817393 chrX 155270560 5157026 0.03321316030546937 0.251500969546292 chrY 59373566 272254 0.004585441271962678 0.14030018203734695