BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082329.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 = 2,046,269 number of mapped reads = 1,823,402 (89.11%) number of supplementary alignments = 15,814 (0.77%) number of secondary alignments = 0 number of mapped bases = 123,586,738 bp number of sequenced bases = 123,541,529 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,137 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5962 >>>>>>> ACTG content number of A's = 35,625,269 bp (28.84%) number of C's = 23,258,330 bp (18.83%) number of T's = 37,990,312 bp (30.75%) number of G's = 26,665,051 bp (21.58%) number of N's = 2,567 bp (0%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,065,777 number of insertions = 10,477 mapped reads with insertion percentage = 0.57% number of deletions = 27,806 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.0399X std coverageData = 0.3793X There is a 3.56% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 9783561 0.03925190220488959 0.6678749671922081 chr2 243199373 10576764 0.043490095675534496 0.45155033100097264 chr3 198022430 8515106 0.04300071461601598 0.2266621322588417 chr4 191154276 8466834 0.04429319697771239 0.23944437211304292 chr5 180915260 7762011 0.042904125389975394 0.22556325953380926 chr6 171115067 7396407 0.04322475588897148 0.26816400317086925 chr7 159138663 6961615 0.04374559185532431 0.5148194984512139 chr8 146364022 6326033 0.0432212295997168 0.6198306143798481 chr9 141213431 5190885 0.03675914509859901 0.3375425538180214 chr10 135534747 5750281 0.042426618467071034 0.35520175125619263 chr11 135006516 5566920 0.04123445419478864 0.3205229914127038 chr12 133851895 5586272 0.0417347247866756 0.22647751667853752 chr13 115169878 4031466 0.03500451741383281 0.20175944756288144 chr14 107349540 3769504 0.03511430044320637 0.22120720840501565 chr15 102531392 3383653 0.03300114173813226 0.20151418468172022 chr16 90354753 3193714 0.03534638626038854 0.2424126333813354 chr17 81195210 2988061 0.03680095168175561 0.22744461805931743 chr18 78077248 3366719 0.04312035946758779 0.6270323432259367 chr19 59128983 2183424 0.03692645956721427 0.5328939600131399 chr20 63025520 2340157 0.03713030848456308 0.21672688166885623 chr21 48129895 1600930 0.033262694630852616 0.2135845004702851 chr22 51304566 1204458 0.02347662389347568 0.16454850679216557 chrMT 16571 919 0.05545833081890049 0.2413358602522028 chrX 155270560 7322756 0.04716126482702194 0.26595001104199006 chrY 59373566 318288 0.0053607694710470985 0.12215054246622718