BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094021.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 422,474 number of mapped reads = 380,092 (89.97%) number of supplementary alignments = 18,803 (4.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 190,971 number of mapped paired reads (second in pair) = 189,121 number of mapped paired reads (both in pair) = 375,916 number of mapped paired reads (singletons) = 4,176 number of mapped bases = 48,246,099 bp number of sequenced bases = 47,195,688 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 353,139 duplication rate = 47.49% >>>>>>> Insert size mean insert size = 642,330.0687 std insert size = 7,207,733.4386 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 45.6787 >>>>>>> ACTG content number of A's = 13,083,920 bp (27.72%) number of C's = 10,531,746 bp (22.32%) number of T's = 12,460,836 bp (26.4%) number of G's = 11,118,755 bp (23.56%) number of N's = 431 bp (0%) GC percentage = 45.87% >>>>>>> Mismatches and indels general error rate = 0.0387 number of mismatches = 1,771,802 number of insertions = 28,282 mapped reads with insertion percentage = 7.32% number of deletions = 137,984 mapped reads with deletion percentage = 35.07% homopolymer indels = 29.45% >>>>>>> Coverage mean coverageData = 0.0156X std coverageData = 4.4125X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 790425 0.0031712057399447763 1.0144733031999669 chr2 243199373 3319994 0.013651326313246705 3.6025091275640935 chr3 198022430 594294 0.0030011448703058537 0.770590803533636 chr4 191154276 528705 0.0027658549474456956 0.7016633617255039 chr5 180915260 898854 0.004968370274569431 1.997204962997935 chr6 171115067 1130276 0.006605356382790068 2.5963085099766117 chr7 159138663 1593104 0.010010791657838674 2.9470342389011996 chr8 146364022 637034 0.004352394743566148 1.1566148806484378 chr9 141213431 381557 0.002701988028320054 0.6822054566906136 chr10 135534747 652527 0.004814462818158357 1.0763190109228433 chr11 135006516 1327312 0.009831466208638404 2.3680269469371784 chr12 133851895 1060665 0.007924168723946717 1.869563027449703 chr13 115169878 996417 0.008651715338276212 1.9336861090053106 chr14 107349540 224920 0.002095211586374753 0.5935846994786848 chr15 102531392 359784 0.0035090131225371446 0.8245709098979574 chr16 90354753 258904 0.0028654164988974073 0.7684712806896774 chr17 81195210 1141422 0.014057750451042617 2.9419749298422655 chr18 78077248 265211 0.003396776997058093 1.130669326373822 chr19 59128983 259929 0.004395966018898042 0.8971240016708915 chr20 63025520 306072 0.004856318519863065 1.6028669632585106 chr21 48129895 204611 0.004251224732570059 1.366410927366032 chr22 51304566 219093 0.004270438619439837 0.7393483140125631 chrMT 16571 5273838 318.2570756140245 1377.1777085084032 chrX 155270560 25352607 0.16328019297412208 10.358796400464014 chrY 59373566 468544 0.007891457959590974 2.081594035498745