BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240015.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,369,500 number of mapped reads = 1,000,596 (73.06%) number of supplementary alignments = 3,910 (0.29%) number of secondary alignments = 0 number of mapped bases = 60,715,842 bp number of sequenced bases = 60,679,713 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 227,002 duplication rate = 13.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1772 >>>>>>> ACTG content number of A's = 16,200,108 bp (26.7%) number of C's = 10,185,177 bp (16.79%) number of T's = 19,425,401 bp (32.01%) number of G's = 14,831,010 bp (24.44%) number of N's = 38,017 bp (0.06%) GC percentage = 41.23% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 640,801 number of insertions = 4,450 mapped reads with insertion percentage = 0.44% number of deletions = 20,119 mapped reads with deletion percentage = 1.99% homopolymer indels = 49.52% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.3414X There is a 0.92% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 4028468 0.01616231880922776 0.3607620103308462 chr2 243199373 6422252 0.026407354265670743 0.413774040132591 chr3 198022430 4623796 0.023349859912334174 0.32661582712897563 chr4 191154276 4402059 0.02302882829573742 0.3271266601913913 chr5 180915260 2941610 0.016259601318318863 0.2548945033461393 chr6 171115067 3482370 0.020351042494697442 0.3175685375950253 chr7 159138663 3675763 0.023097862773925656 0.6000559388972154 chr8 146364022 3946870 0.026966121496715907 0.44150432677104606 chr9 141213431 2392007 0.01693894825060939 0.3014135398228209 chr10 135534747 2068243 0.015259872805901206 0.26775474607551636 chr11 135006516 2701942 0.0200134192041516 0.307717899926219 chr12 133851895 2805868 0.020962482451219684 0.30470542879537493 chr13 115169878 1431012 0.012425228061802757 0.22725005172439247 chr14 107349540 2412220 0.022470706441778884 0.31838615507274637 chr15 102531392 1322921 0.012902594748738026 0.23521188183002084 chr16 90354753 1391615 0.015401680086491964 0.24761486803791755 chr17 81195210 1887178 0.023242479451681942 0.32271232089940277 chr18 78077248 1803420 0.023097894024133637 0.4215592234706742 chr19 59128983 988499 0.016717672955748282 0.3172063600011906 chr20 63025520 1068843 0.01695889220747405 0.26022474846898275 chr21 48129895 1028525 0.02136977444060495 0.31432387558191915 chr22 51304566 648258 0.012635483555206373 0.22944381088583052 chrMT 16571 63737 3.8462977490797177 4.125877580309297 chrX 155270560 3045930 0.019616919008986634 0.2962607919937783 chrY 59373566 132436 0.0022305549240549238 0.07254050012614556