BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082328.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,313,527 number of mapped reads = 2,997,332 (90.46%) number of supplementary alignments = 29,870 (0.9%) number of secondary alignments = 0 number of mapped bases = 202,984,843 bp number of sequenced bases = 202,913,126 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,385 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2125 >>>>>>> ACTG content number of A's = 57,739,088 bp (28.46%) number of C's = 38,178,721 bp (18.82%) number of T's = 62,876,048 bp (30.99%) number of G's = 44,115,129 bp (21.74%) number of N's = 4,140 bp (0%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,691,654 number of insertions = 16,331 mapped reads with insertion percentage = 0.54% number of deletions = 44,547 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.0656X std coverageData = 0.5312X There is a 5.58% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15974095 0.06408848626298909 0.9280073144978789 chr2 243199373 17387172 0.07149349024020715 0.6284456449251993 chr3 198022430 13990438 0.07065077425824944 0.2999747308783687 chr4 191154276 13681813 0.07157471591166499 0.31487866434304845 chr5 180915260 12850883 0.07103260941061577 0.30521021597142317 chr6 171115067 12225180 0.07144420543633367 0.3882379594886246 chr7 159138663 11229298 0.0705629781494394 0.678876054788439 chr8 146364022 10553653 0.07210551374435446 1.019806516222363 chr9 141213431 8452130 0.05985358432371776 0.4521231085934411 chr10 135534747 9335178 0.06887664017257508 0.46296863902571733 chr11 135006516 9121926 0.06756656100954417 0.4320056856814147 chr12 133851895 9145633 0.06832651117864263 0.3034036937697877 chr13 115169878 6741563 0.05853581784639904 0.27218825990582607 chr14 107349540 6214165 0.05788720659632077 0.29492230557728605 chr15 102531392 5751718 0.056097141449128085 0.2719742269926575 chr16 90354753 5295189 0.05860443224276204 0.31227680761802984 chr17 81195210 4940711 0.06084978411903855 0.31711335990351885 chr18 78077248 5431248 0.06956249277638474 0.8431681738111779 chr19 59128983 3613207 0.061107206934372604 0.7129692376778555 chr20 63025520 3910356 0.06204401010892096 0.29009560537639323 chr21 48129895 2679415 0.0556704933596884 0.2864198997231179 chr22 51304566 2092345 0.040782822332031815 0.22584977654268004 chrMT 16571 1546 0.09329551626335164 0.33320141201708664 chrX 155270560 11876353 0.0764881185461043 0.36522851652737875 chrY 59373566 489628 0.00824656548336679 0.15742563960819028