BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084861.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 = 2,356,000 number of mapped reads = 2,115,644 (89.8%) number of supplementary alignments = 14,685 (0.62%) number of secondary alignments = 0 number of mapped bases = 144,804,696 bp number of sequenced bases = 144,749,083 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,081 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6009 >>>>>>> ACTG content number of A's = 41,279,922 bp (28.52%) number of C's = 26,429,665 bp (18.26%) number of T's = 46,500,636 bp (32.12%) number of G's = 30,516,214 bp (21.08%) number of N's = 22,646 bp (0.02%) GC percentage = 39.34% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,144,431 number of insertions = 11,238 mapped reads with insertion percentage = 0.53% number of deletions = 31,547 mapped reads with deletion percentage = 1.48% homopolymer indels = 49.21% >>>>>>> Coverage mean coverageData = 0.0468X std coverageData = 0.3022X There is a 3.96% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.09% 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% 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 12548594 0.05034528680271573 0.4363882024898265 chr2 243199373 12167991 0.05003298672155705 0.3525264162353587 chr3 198022430 9844807 0.04971561554920824 0.25364039171125513 chr4 191154276 8783258 0.045948530076303395 0.24640461742484232 chr5 180915260 7943659 0.04390817557347014 0.24060135976234917 chr6 171115067 7970910 0.04658216333457065 0.24955608022531153 chr7 159138663 7934015 0.049855986285369254 0.31270059262979083 chr8 146364022 8158130 0.05573862953834379 0.42423930187682996 chr9 141213431 9332823 0.0660901936445408 0.3612518861955466 chr10 135534747 4133008 0.030494084295593957 0.2261451095785212 chr11 135006516 6679674 0.04947667859231328 0.27320711261890734 chr12 133851895 6531437 0.04879599948883802 0.25420968603767036 chr13 115169878 3429736 0.029779800582926726 0.19556762640727995 chr14 107349540 3113593 0.029004250973036307 0.1977094480856255 chr15 102531392 4278781 0.04173142406961568 0.23219552719734005 chr16 90354753 3117460 0.034502446152445354 0.22393183774603798 chr17 81195210 4845546 0.05967773222090318 0.28238735790922287 chr18 78077248 5482408 0.07021774128104515 0.4917587819713631 chr19 59128983 2983936 0.05046486255310699 0.3419074234342911 chr20 63025520 2943493 0.04670319261150087 0.25017192271325694 chr21 48129895 1237480 0.025711254927940318 0.18933493529304793 chr22 51304566 1587074 0.030934361670655202 0.1986020135094057 chrMT 16571 90442 5.457848047794339 3.4634239863767227 chrX 155270560 9354717 0.06024784737042231 0.29008310724341335 chrY 59373566 311724 0.005250215222040057 0.11609436813644411