BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038468.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,406,848 number of mapped reads = 13,803,521 (95.81%) number of supplementary alignments = 265,933 (1.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,964,652 number of mapped paired reads (second in pair) = 6,838,869 number of mapped paired reads (both in pair) = 13,654,782 number of mapped paired reads (singletons) = 148,739 number of mapped bases = 1,985,879,947 bp number of sequenced bases = 1,984,395,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,315,046 duplication rate = 9.54% >>>>>>> Insert size mean insert size = 78,928.3605 std insert size = 2,638,866.4158 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 53.7109 >>>>>>> ACTG content number of A's = 586,003,041 bp (29.53%) number of C's = 402,107,237 bp (20.26%) number of T's = 585,053,655 bp (29.48%) number of G's = 411,187,930 bp (20.72%) number of N's = 43,991 bp (0%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 28,434,051 number of insertions = 382,088 mapped reads with insertion percentage = 2.59% number of deletions = 713,204 mapped reads with deletion percentage = 4.96% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.6415X std coverageData = 11.6845X There is a 26.1% of reference with a coverageData >= 1X There is a 14.26% of reference with a coverageData >= 2X There is a 7.33% of reference with a coverageData >= 3X There is a 4.27% of reference with a coverageData >= 4X There is a 2.42% of reference with a coverageData >= 5X There is a 1.45% of reference with a coverageData >= 6X There is a 0.88% of reference with a coverageData >= 7X There is a 0.55% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 120604598 0.48386879645928743 17.70189964893303 chr2 243199373 219458176 0.9023796948687035 15.105992438288713 chr3 198022430 109534706 0.5531429242636806 1.3476198911974024 chr4 191154276 119506606 0.6251840581374177 10.847413969585286 chr5 180915260 117086524 0.6471898722086794 1.5678520641363307 chr6 171115067 140859775 0.8231874461411396 16.674407289066803 chr7 159138663 107439370 0.6751305306618041 9.409173978033833 chr8 146364022 101879178 0.6960670840269749 3.2601209107093734 chr9 141213431 73867166 0.5230888129897503 18.557688816515682 chr10 135534747 92294852 0.6809681948201814 22.190700526523678 chr11 135006516 110420625 0.8178910786794913 8.87654873541835 chr12 133851895 65032237 0.48585219506978217 1.2768041253651445 chr13 115169878 129335492 1.122997560178018 2.0720870144900476 chr14 107349540 35161866 0.32754556749847274 1.2087719550201053 chr15 102531392 31750428 0.3096654339775276 0.9129592799267809 chr16 90354753 77709351 0.8600471853428674 15.53472137735353 chr17 81195210 49905074 0.6146307645487954 8.315530152490716 chr18 78077248 30189690 0.38666437116226227 15.300385863123434 chr19 59128983 25895685 0.4379524843172087 9.464890946764902 chr20 63025520 56085204 0.8898808609591797 3.647940493854849 chr21 48129895 17540739 0.3644458189655307 5.19296211159995 chr22 51304566 9487405 0.18492320936892828 0.7928323810691967 chrMT 16571 967580 58.3899583609921 34.76365062191288 chrX 155270560 104656260 0.6740251339339537 2.632185749013061 chrY 59373566 39211360 0.6604178027642806 18.866136047212482