BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173873.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 = 2,504,024 number of mapped reads = 2,434,281 (97.21%) number of supplementary alignments = 249,252 (9.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,218,502 number of mapped paired reads (second in pair) = 1,215,779 number of mapped paired reads (both in pair) = 2,390,442 number of mapped paired reads (singletons) = 43,839 number of mapped bases = 287,157,070 bp number of sequenced bases = 287,000,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,903,590 duplication rate = 64.94% >>>>>>> Insert size mean insert size = 992,075.9055 std insert size = 9,268,426.2497 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.8861 >>>>>>> ACTG content number of A's = 86,741,715 bp (30.22%) number of C's = 55,904,107 bp (19.48%) number of T's = 86,515,636 bp (30.14%) number of G's = 57,835,475 bp (20.15%) number of N's = 3,630 bp (0%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 3,010,395 number of insertions = 31,435 mapped reads with insertion percentage = 1.25% number of deletions = 63,092 mapped reads with deletion percentage = 2.53% homopolymer indels = 42.86% >>>>>>> Coverage mean coverageData = 0.0928X std coverageData = 1.5011X There is a 1.94% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 1.18% of reference with a coverageData >= 3X There is a 0.98% of reference with a coverageData >= 4X There is a 0.75% of reference with a coverageData >= 5X There is a 0.6% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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% 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 22048682 0.08845988792942666 1.086483616889433 chr2 243199373 25192858 0.10358932134253487 4.05395535900845 chr3 198022430 22104369 0.11162558201108834 0.9694459755702691 chr4 191154276 17279702 0.09039662811414169 1.0275580175034877 chr5 180915260 19801446 0.10945149679468719 0.9702751318841605 chr6 171115067 17390566 0.10163082833611607 1.0012903895792848 chr7 159138663 15305132 0.09617481830923764 1.1564995432067702 chr8 146364022 14210795 0.09709213238209592 1.4211522922068713 chr9 141213431 12232267 0.08662254654799798 1.0578048540910074 chr10 135534747 14039528 0.1035861895990406 1.2636959132259051 chr11 135006516 13822945 0.10238724329424219 0.9354239560114922 chr12 133851895 12174050 0.0909516447264344 0.8810238232335169 chr13 115169878 9164498 0.07957374062686773 0.8214442637736202 chr14 107349540 8984420 0.08369313925332143 0.8368131530192178 chr15 102531392 8320165 0.08114748895635787 0.8153290781305729 chr16 90354753 8358346 0.0925058806812299 0.9910154513344016 chr17 81195210 10668338 0.13139122369410708 1.089854632887921 chr18 78077248 8307711 0.10640373748828852 1.4136387530987908 chr19 59128983 4326058 0.07316307131478991 0.8883822805749102 chr20 63025520 6136158 0.09735989484894372 0.9094565875448973 chr21 48129895 3696062 0.07679347731799539 0.9005882733468543 chr22 51304566 3390231 0.06608049271871826 0.7469245203376251 chrMT 16571 535768 32.331663749924566 28.3448381304591 chrX 155270560 7495680 0.04827495952870911 0.6362013107605138 chrY 59373566 2171295 0.03657006217211208 0.6706080516489732