BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818917.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,500,363 number of mapped reads = 2,408,446 (96.32%) number of supplementary alignments = 37,077 (1.48%) number of secondary alignments = 0 number of mapped bases = 223,333,238 bp number of sequenced bases = 223,188,311 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 660,236 duplication rate = 22.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2893 >>>>>>> ACTG content number of A's = 65,029,968 bp (29.14%) number of C's = 44,217,094 bp (19.81%) number of T's = 64,537,855 bp (28.92%) number of G's = 49,400,403 bp (22.13%) number of N's = 2,991 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,411,584 number of insertions = 36,229 mapped reads with insertion percentage = 1.46% number of deletions = 74,276 mapped reads with deletion percentage = 3.01% homopolymer indels = 40.87% >>>>>>> Coverage mean coverageData = 0.0721X std coverageData = 0.8979X There is a 4.57% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 20577888 0.0825590239953705 1.4360183858251154 chr2 243199373 16484906 0.06778350534645498 1.328031870474219 chr3 198022430 12919395 0.06524207888975002 0.3697872733842775 chr4 191154276 12965952 0.06782977745159098 0.5249364985416914 chr5 180915260 11878132 0.06565577718540713 0.3999605958450233 chr6 171115067 10768778 0.06293296194659469 0.40639089090470515 chr7 159138663 19750704 0.12411002849760024 1.9949685841230111 chr8 146364022 19073290 0.13031406037748813 0.6707738951755234 chr9 141213431 7989461 0.05657720333981546 0.7581877982527291 chr10 135534747 9925220 0.0732300773026123 1.0966523926372984 chr11 135006516 9420719 0.0697797356684621 0.4952683163504355 chr12 133851895 8510509 0.06358153539776183 0.37632210096073293 chr13 115169878 5132125 0.044561347889940456 0.30024294493804904 chr14 107349540 7028873 0.06547650786393681 0.4125631625217489 chr15 102531392 5950527 0.05803614760248257 0.3446948960677071 chr16 90354753 5441424 0.06022288611646141 0.8869657744350825 chr17 81195210 5629991 0.06933895484721328 0.5314129883571873 chr18 78077248 3908209 0.05005567050723919 0.8430468848959071 chr19 59128983 4251659 0.07190482203964171 1.1866896616816072 chr20 63025520 8962733 0.14220799764920622 0.607005898776558 chr21 48129895 2702718 0.056154662294609206 0.43055125510285913 chr22 51304566 2598070 0.05064013210831956 0.358521546234449 chrMT 16571 289161 17.449821978154606 10.921484534954859 chrX 155270560 10322906 0.06648334365510114 0.4729672626169755 chrY 59373566 849888 0.014314248869606383 1.0417728449220014