BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094086.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 = 316,718 number of mapped reads = 301,882 (95.32%) number of supplementary alignments = 10,793 (3.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 151,759 number of mapped paired reads (second in pair) = 150,123 number of mapped paired reads (both in pair) = 299,492 number of mapped paired reads (singletons) = 2,390 number of mapped bases = 40,197,254 bp number of sequenced bases = 39,372,716 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 284,408 duplication rate = 49.01% >>>>>>> Insert size mean insert size = 482,219.2893 std insert size = 6,212,200.7379 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 39.953 >>>>>>> ACTG content number of A's = 10,349,893 bp (26.29%) number of C's = 9,375,717 bp (23.81%) number of T's = 9,932,963 bp (25.23%) number of G's = 9,713,816 bp (24.67%) number of N's = 327 bp (0%) GC percentage = 48.48% >>>>>>> Mismatches and indels general error rate = 0.0386 number of mismatches = 1,464,962 number of insertions = 23,262 mapped reads with insertion percentage = 7.57% number of deletions = 118,716 mapped reads with deletion percentage = 37.49% homopolymer indels = 28.04% >>>>>>> Coverage mean coverageData = 0.013X std coverageData = 3.6322X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% 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% 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 269232 0.0010801658143110503 0.38958430267860095 chr2 243199373 2097504 0.008624627498525664 3.871664522054681 chr3 198022430 768741 0.0038820905288355465 1.7814780907999659 chr4 191154276 515538 0.0026969734121982183 1.1107131454222765 chr5 180915260 301768 0.001668007441716083 0.7207242098148754 chr6 171115067 948597 0.00554362053927139 2.994080528120354 chr7 159138663 1197803 0.0075267881319324645 2.9081209180609795 chr8 146364022 608872 0.00415998407040222 1.78511574771997 chr9 141213431 453789 0.0032134974469956758 1.5054357217683472 chr10 135534747 699203 0.005158846830621228 1.9370236120721551 chr11 135006516 1241024 0.009192326687402259 2.4820217194911707 chr12 133851895 1193725 0.008918252520817878 4.041918935320105 chr13 115169878 1077893 0.009359157261588834 2.6251077210766747 chr14 107349540 198357 0.001847767582422803 0.8329475241709368 chr15 102531392 647915 0.0063191866155489235 2.206918695879405 chr16 90354753 197380 0.002184500465625754 0.5450634916864974 chr17 81195210 868084 0.010691320337739136 3.0031163399825793 chr18 78077248 117485 0.0015047277281084498 0.5603032196789999 chr19 59128983 120387 0.0020360066061004298 0.5406743308706398 chr20 63025520 242504 0.0038477112128547293 1.2412089813360978 chr21 48129895 616536 0.012809834719149087 5.386144946711934 chr22 51304566 77171 0.001504174111910429 0.44484505042584743 chrMT 16571 1340285 80.8813590006638 387.1687778617689 chrX 155270560 24045368 0.15486108892761127 12.066756356034725 chrY 59373566 352093 0.005930130590438175 1.4778997169018302