BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085032.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 = 2,544,833 number of mapped reads = 2,323,785 (91.31%) number of supplementary alignments = 15,710 (0.62%) number of secondary alignments = 0 number of mapped bases = 156,298,270 bp number of sequenced bases = 156,243,876 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,602 duplication rate = 2.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2808 >>>>>>> ACTG content number of A's = 43,544,804 bp (27.87%) number of C's = 30,128,674 bp (19.28%) number of T's = 47,870,631 bp (30.64%) number of G's = 34,695,939 bp (22.21%) number of N's = 3,828 bp (0%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,277,146 number of insertions = 10,829 mapped reads with insertion percentage = 0.46% number of deletions = 31,637 mapped reads with deletion percentage = 1.35% homopolymer indels = 46.82% >>>>>>> Coverage mean coverageData = 0.0505X std coverageData = 0.364X There is a 4.32% of reference with a coverageData >= 1X There is a 0.55% 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 13754398 0.05518300393722991 0.5216247314776594 chr2 243199373 15158646 0.06233011957641848 0.49442564025787133 chr3 198022430 9682315 0.04889504183945223 0.253225052328542 chr4 191154276 9028529 0.04723163503807783 0.25027032173496705 chr5 180915260 7932763 0.0438479484815156 0.23693890990758626 chr6 171115067 10888169 0.06363068542643296 0.35857908339594047 chr7 159138663 13840719 0.08697269877151098 0.41646272484463354 chr8 146364022 9500107 0.06490739233716876 0.5837045293468646 chr9 141213431 5211798 0.03690724007690175 0.3269637604413742 chr10 135534747 10974591 0.08097252728851886 0.49833142776416767 chr11 135006516 6057856 0.044870841641450845 0.32540828010303935 chr12 133851895 6522177 0.04872681854821704 0.25409186954640023 chr13 115169878 3121278 0.0271015134703885 0.18564805865727374 chr14 107349540 5275012 0.049138654902480254 0.26654077483783045 chr15 102531392 2667543 0.026016841749305422 0.19153550304239578 chr16 90354753 4280114 0.04737010348531416 0.25968401578442457 chr17 81195210 2479680 0.030539732577820784 0.21035721080746647 chr18 78077248 3674822 0.047066489843494486 0.5262494411661112 chr19 59128983 2383571 0.04031138164510626 0.3928773473631328 chr20 63025520 3689032 0.05853235324357498 0.2791003438971508 chr21 48129895 1757722 0.03652037886224352 0.22482480172211333 chr22 51304566 1157104 0.02255362612364755 0.1671371422945976 chrMT 16571 16808 1.014302094019673 1.3099105669100457 chrX 155270560 6939438 0.044692554725119814 0.2655468086031509 chrY 59373566 304078 0.005121437375009613 0.10179428876856594