BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240229.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,794,064 number of mapped reads = 1,379,571 (76.9%) number of supplementary alignments = 7,546 (0.42%) number of secondary alignments = 0 number of mapped bases = 83,912,109 bp number of sequenced bases = 83,870,982 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,437 duplication rate = 9.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7721 >>>>>>> ACTG content number of A's = 22,038,681 bp (26.28%) number of C's = 14,735,219 bp (17.57%) number of T's = 27,308,467 bp (32.56%) number of G's = 19,768,228 bp (23.57%) number of N's = 20,387 bp (0.02%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 745,471 number of insertions = 5,460 mapped reads with insertion percentage = 0.39% number of deletions = 23,939 mapped reads with deletion percentage = 1.72% homopolymer indels = 48.62% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.2711X There is a 1.98% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 5800825 0.02327306137383706 0.36067024922554564 chr2 243199373 5902973 0.024272155504282487 0.35792001591410016 chr3 198022430 7765055 0.03921300733457316 0.2613933646932833 chr4 191154276 4865885 0.025455276762943038 0.21266161086659724 chr5 180915260 4500466 0.02487609945120163 0.2070105988392407 chr6 171115067 5848252 0.034177305964529704 0.30381693894299283 chr7 159138663 3901246 0.02451475918205999 0.30846184975032026 chr8 146364022 4944125 0.033779647022818216 0.3314258519460945 chr9 141213431 2647219 0.018746226766489373 0.24288356733870875 chr10 135534747 3631351 0.02679276776161319 0.24125418549948202 chr11 135006516 3245007 0.02403592875472766 0.22200859976223358 chr12 133851895 4363394 0.03259867183800424 0.23793731339054403 chr13 115169878 2540469 0.022058450040209298 0.19427798727796988 chr14 107349540 2236096 0.020830047338814866 0.19474164097463642 chr15 102531392 2959886 0.028868095343911843 0.23106303884007956 chr16 90354753 2323260 0.025712648453590482 0.2128324539973233 chr17 81195210 2322070 0.02859860821839121 0.23543131303029613 chr18 78077248 3826935 0.04901472705595361 0.3869496473670632 chr19 59128983 1576740 0.026666110594190332 0.30444946744638607 chr20 63025520 1850890 0.029367310257813025 0.2271259069004603 chr21 48129895 1546440 0.03213055004587066 0.2391814213307138 chr22 51304566 746990 0.014559912659625656 0.15530586955229944 chrMT 16571 37360 2.2545410657172167 2.89878107991053 chrX 155270560 4324945 0.027854250026534327 0.23806432294087906 chrY 59373566 204230 0.0034397462331974466 0.08315096055687429