BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080776.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 = 2,723,367 number of mapped reads = 2,399,270 (88.1%) number of supplementary alignments = 22,864 (0.84%) number of secondary alignments = 0 number of mapped bases = 160,456,122 bp number of sequenced bases = 160,400,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,193 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3406 >>>>>>> ACTG content number of A's = 45,473,560 bp (28.35%) number of C's = 30,960,043 bp (19.3%) number of T's = 49,022,622 bp (30.56%) number of G's = 34,941,097 bp (21.78%) number of N's = 3,232 bp (0%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,194,123 number of insertions = 11,994 mapped reads with insertion percentage = 0.5% number of deletions = 34,896 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.89% >>>>>>> Coverage mean coverageData = 0.0518X std coverageData = 0.3552X There is a 3.96% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 19596248 0.07862065868233083 0.5758766771366333 chr2 243199373 10119022 0.04160792799412357 0.39655189519907036 chr3 198022430 9678991 0.04887825586222733 0.2764814699058871 chr4 191154276 10242509 0.05358242156194298 0.2990809538745576 chr5 180915260 13999218 0.07737997336432538 0.35068889686870947 chr6 171115067 10475380 0.06121833795033374 0.3598757557084048 chr7 159138663 12441153 0.07817806663362505 0.46435806671138463 chr8 146364022 7721305 0.052754118768340484 0.4387205189260638 chr9 141213431 5568319 0.03943193618742965 0.2829001501485726 chr10 135534747 5981870 0.04413532420582893 0.3013211114935147 chr11 135006516 6600287 0.048888655122394244 0.2979160509652804 chr12 133851895 6315451 0.04718238019715746 0.2735726858462797 chr13 115169878 6577329 0.05710980261696552 0.3025947375094064 chr14 107349540 4105588 0.03824504511151142 0.25087109807266833 chr15 102531392 4241980 0.04137249984863173 0.26266861981192147 chr16 90354753 3676020 0.04068430135601168 0.25912897896841836 chr17 81195210 3704602 0.04562586881664571 0.27605658354699464 chr18 78077248 2079704 0.026636492105869304 0.3905728147669525 chr19 59128983 2204170 0.03727731965219155 0.41021418848534363 chr20 63025520 2820377 0.04474976168383855 0.26914648429209936 chr21 48129895 2497019 0.051880832069132916 0.2939354394089626 chr22 51304566 846340 0.016496387475531903 0.15571309619375906 chrMT 16571 15782 0.9523866996560256 1.2872239222118202 chrX 155270560 8578640 0.055249623624723194 0.3070038592468724 chrY 59373566 368818 0.0062118216042472505 0.13115919945269214