BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472398.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,818,552 number of mapped reads = 18,547,970 (98.56%) number of supplementary alignments = 83,469 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,328,893 number of mapped paired reads (second in pair) = 9,219,077 number of mapped paired reads (both in pair) = 18,374,774 number of mapped paired reads (singletons) = 173,196 number of mapped bases = 1,820,232,199 bp number of sequenced bases = 1,820,008,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,240,547 duplication rate = 46.46% >>>>>>> Insert size mean insert size = 26,127.6376 std insert size = 1,584,666.0838 median insert size = 263 >>>>>>> Mapping quality mean mapping quality = 54.7896 >>>>>>> ACTG content number of A's = 498,684,154 bp (27.4%) number of C's = 413,241,990 bp (22.71%) number of T's = 498,037,627 bp (27.36%) number of G's = 409,827,444 bp (22.52%) number of N's = 217,396 bp (0.01%) GC percentage = 45.22% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 12,149,743 number of insertions = 113,334 mapped reads with insertion percentage = 0.6% number of deletions = 92,681 mapped reads with deletion percentage = 0.49% homopolymer indels = 46.08% >>>>>>> Coverage mean coverageData = 0.588X std coverageData = 16.3732X There is a 5.1% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.54% of reference with a coverageData >= 6X There is a 0.5% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.44% of reference with a coverageData >= 10X There is a 0.42% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.4% of reference with a coverageData >= 13X There is a 0.39% of reference with a coverageData >= 14X There is a 0.38% of reference with a coverageData >= 15X There is a 0.37% of reference with a coverageData >= 16X There is a 0.36% of reference with a coverageData >= 17X There is a 0.35% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.33% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.32% of reference with a coverageData >= 22X There is a 0.31% of reference with a coverageData >= 23X There is a 0.31% of reference with a coverageData >= 24X There is a 0.3% of reference with a coverageData >= 25X There is a 0.3% of reference with a coverageData >= 26X There is a 0.29% of reference with a coverageData >= 27X There is a 0.29% of reference with a coverageData >= 28X There is a 0.28% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.25% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187356019 0.7516772405554006 20.23100290024289 chr2 243199373 171438285 0.7049289761121218 19.96262199264659 chr3 198022430 132036095 0.6667734306664149 13.622687633511193 chr4 191154276 50385715 0.26358664872346355 9.955051339735615 chr5 180915260 69596766 0.3846926234967686 11.918747084794793 chr6 171115067 141787902 0.82861143957592 21.670868967721606 chr7 159138663 140306868 0.8816642376843394 22.466363597319262 chr8 146364022 87778276 0.5997257714057626 14.597270301351603 chr9 141213431 57941743 0.4103132583755436 9.78096307973008 chr10 135534747 36033865 0.26586440597406363 9.726111618316132 chr11 135006516 52759726 0.3907939228651749 10.808731755706853 chr12 133851895 97840777 0.7309629572297053 17.72905600610291 chr13 115169878 72338351 0.6281013078784368 21.828510639481035 chr14 107349540 26166303 0.24374862714828588 6.974980153035347 chr15 102531392 28991154 0.2827539296452739 8.063678079183951 chr16 90354753 115987571 1.283690864607864 28.566343765988144 chr17 81195210 90656647 1.1165270340454811 22.72957117039656 chr18 78077248 20016610 0.2563693074837884 7.00578422678757 chr19 59128983 59580884 1.0076426310258033 19.433308944423786 chr20 63025520 57349522 0.9099412745821058 20.018382217253542 chr21 48129895 14084861 0.2926426704234447 13.495713191877934 chr22 51304566 20992680 0.4091776158870538 11.60479632279537 chrMT 16571 29607 1.7866755174702793 2.080838930044501 chrX 155270560 88473348 0.5698011780211265 12.367115652207296 chrY 59373566 302624 0.005096948362508662 0.36360353289117947