BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054572.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 13,923,030 number of mapped reads = 10,155,512 (72.94%) number of supplementary alignments = 328 (0%) number of secondary alignments = 0 number of mapped bases = 476,410,563 bp number of sequenced bases = 476,312,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,404,531 duplication rate = 22.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1446 >>>>>>> ACTG content number of A's = 144,051,318 bp (30.24%) number of C's = 94,701,609 bp (19.88%) number of T's = 138,471,939 bp (29.07%) number of G's = 98,905,536 bp (20.76%) number of N's = 182,125 bp (0.04%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 2,736,807 number of insertions = 20,985 mapped reads with insertion percentage = 0.21% number of deletions = 65,771 mapped reads with deletion percentage = 0.65% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.1539X std coverageData = 1.3648X There is a 4.83% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 1.53% of reference with a coverageData >= 3X There is a 1.1% of reference with a coverageData >= 4X There is a 0.84% of reference with a coverageData >= 5X There is a 0.66% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 38690174 0.15522598838379625 1.409977874558016 chr2 243199373 56360864 0.23174757115841743 1.799416972307346 chr3 198022430 35610963 0.17983297649665242 1.4324576700281004 chr4 191154276 19647001 0.10278086062798826 1.0459249008539697 chr5 180915260 29531686 0.16323490898446047 1.3664431932377792 chr6 171115067 27401717 0.1601362023836276 1.408273513375914 chr7 159138663 23268063 0.14621250776751846 1.3427269543685734 chr8 146364022 31805882 0.21730669576707862 1.6995541063373023 chr9 141213431 23069943 0.16336932568404205 1.3612953444186315 chr10 135534747 16188528 0.11944190223042951 1.18591988416456 chr11 135006516 23252583 0.17223304244070708 1.4538463794897443 chr12 133851895 24083038 0.17992302611778488 1.4220360661887224 chr13 115169878 11204828 0.09728957080253224 0.9938925898282179 chr14 107349540 8790564 0.08188730012257156 1.0258861633205794 chr15 102531392 10009612 0.09762485229889398 0.9758648972526094 chr16 90354753 11672674 0.12918716074626424 1.1854470950400635 chr17 81195210 10369696 0.12771314958111446 1.1484313840047604 chr18 78077248 15179679 0.19441872490177933 1.5833070972185073 chr19 59128983 9259163 0.15659263072392096 1.408356360318745 chr20 63025520 10197396 0.16179788758585412 1.3518176295117077 chr21 48129895 4496244 0.09341894471201319 1.0027495278554577 chr22 51304566 5855888 0.1141397044465789 1.1010173028069474 chrMT 16571 90583 5.466356888540221 11.940202435049349 chrX 155270560 29340716 0.18896509422005048 1.5206605695424626 chrY 59373566 1033078 0.017399628649557616 0.3611965101330671