BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173911.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,987,290 number of mapped reads = 4,871,803 (97.68%) number of supplementary alignments = 502,057 (10.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,438,280 number of mapped paired reads (second in pair) = 2,433,523 number of mapped paired reads (both in pair) = 4,792,284 number of mapped paired reads (singletons) = 79,519 number of mapped bases = 578,270,974 bp number of sequenced bases = 577,922,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,809,137 duplication rate = 64.6% >>>>>>> Insert size mean insert size = 884,550.4384 std insert size = 8,531,371.7766 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 52.6336 >>>>>>> ACTG content number of A's = 173,296,369 bp (29.99%) number of C's = 113,752,853 bp (19.68%) number of T's = 172,985,641 bp (29.93%) number of G's = 117,880,218 bp (20.4%) number of N's = 6,941 bp (0%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 5,955,463 number of insertions = 63,012 mapped reads with insertion percentage = 1.25% number of deletions = 139,800 mapped reads with deletion percentage = 2.8% homopolymer indels = 42.53% >>>>>>> Coverage mean coverageData = 0.1868X std coverageData = 2.7845X There is a 3.88% of reference with a coverageData >= 1X There is a 3.06% of reference with a coverageData >= 2X There is a 2.37% of reference with a coverageData >= 3X There is a 1.96% of reference with a coverageData >= 4X There is a 1.5% of reference with a coverageData >= 5X There is a 1.21% of reference with a coverageData >= 6X There is a 0.9% of reference with a coverageData >= 7X There is a 0.72% of reference with a coverageData >= 8X There is a 0.53% of reference with a coverageData >= 9X There is a 0.44% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 52193147 0.20940026865569975 2.462367506579282 chr2 243199373 53365939 0.2194328806925008 7.782684030023013 chr3 198022430 41819284 0.2111845814638271 1.336114473749588 chr4 191154276 33848638 0.1770749716318143 1.660542956996814 chr5 180915260 36253955 0.200391912766231 1.289623996718467 chr6 171115067 34346580 0.20072212577282864 1.3647163749294848 chr7 159138663 40697770 0.2557377901308622 2.59422711173034 chr8 146364022 25948529 0.17728761922106787 1.4356211257609588 chr9 141213431 25520565 0.18072335484859087 1.5791685939535907 chr10 135534747 24605742 0.18154563714941674 3.2226160030616695 chr11 135006516 28732617 0.2128239276984231 1.35736019684617 chr12 133851895 19493661 0.1456360479618163 1.0938796521055825 chr13 115169878 18947469 0.16451757463874364 1.179006194510836 chr14 107349540 15705252 0.1463001331910691 1.0984415719036662 chr15 102531392 14037009 0.13690450042851265 1.0431199139393244 chr16 90354753 25088663 0.2776684365458893 2.4361755931543456 chr17 81195210 14713481 0.18121119460125787 1.4404682541854026 chr18 78077248 7065402 0.090492456906268 2.044205035473195 chr19 59128983 9318250 0.15759192069987066 2.591472247455519 chr20 63025520 17492216 0.27754179576780963 1.5360526735484465 chr21 48129895 9074596 0.18854385616257838 1.3498885270863574 chr22 51304566 4427685 0.08630196774298803 0.8021277691083495 chrMT 16571 1996136 120.45959809305413 97.30851859470029 chrX 155270560 22680428 0.14607036903840626 1.1047034367953197 chrY 59373566 897960 0.015123902108221022 0.6921931800261744