BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084820.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 = 2,367,204 number of mapped reads = 2,186,187 (92.35%) number of supplementary alignments = 24,767 (1.05%) number of secondary alignments = 0 number of mapped bases = 148,114,683 bp number of sequenced bases = 148,057,772 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,191 duplication rate = 4.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4502 >>>>>>> ACTG content number of A's = 41,569,776 bp (28.08%) number of C's = 27,092,919 bp (18.3%) number of T's = 47,397,101 bp (32.01%) number of G's = 31,977,054 bp (21.6%) number of N's = 20,922 bp (0.01%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,152,275 number of insertions = 12,192 mapped reads with insertion percentage = 0.55% number of deletions = 34,680 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.72% >>>>>>> Coverage mean coverageData = 0.0478X std coverageData = 0.3303X There is a 3.93% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 14406085 0.057797589198383584 0.451736690894482 chr2 243199373 12494852 0.05137699100893652 0.4717127748600588 chr3 198022430 11487701 0.05801212014214753 0.28346367533670147 chr4 191154276 9068271 0.047439540405572724 0.2675602169104212 chr5 180915260 8213101 0.045397502676114775 0.25141856495314774 chr6 171115067 7965008 0.04654767192417954 0.26928505231829236 chr7 159138663 9530329 0.05988694903136141 0.3662864672395003 chr8 146364022 6712102 0.04585896115918432 0.4752978536586453 chr9 141213431 11075428 0.07843041502192521 0.39157283373302093 chr10 135534747 4351308 0.03210474137676297 0.22234294682772765 chr11 135006516 5934846 0.043959700434014606 0.2843076441395833 chr12 133851895 5791067 0.04326473674504197 0.24501483371742713 chr13 115169878 4127448 0.03583791240970143 0.22270553358748565 chr14 107349540 2554133 0.0237926776397924 0.18898684932521828 chr15 102531392 3626169 0.03536642709386019 0.23004989827388092 chr16 90354753 2274813 0.025176461939971216 0.20168976084567708 chr17 81195210 3912662 0.04818833524785514 0.26598333486606857 chr18 78077248 6959399 0.08913478866468244 0.5584355478619698 chr19 59128983 2440881 0.04128061867730754 0.2998118908578606 chr20 63025520 3039756 0.048230558034269295 0.26004024271452 chr21 48129895 1418850 0.02947959890625151 0.20856105446936976 chr22 51304566 1194677 0.023285978094035528 0.17531729765865375 chrMT 16571 67668 4.083519401363828 3.109385926219593 chrX 155270560 9159064 0.05898776947800021 0.29910126548815863 chrY 59373566 309065 0.005205430982535225 0.10156794945650736