BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094150.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 = 448,722 number of mapped reads = 410,674 (91.52%) number of supplementary alignments = 27,807 (6.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 206,248 number of mapped paired reads (second in pair) = 204,426 number of mapped paired reads (both in pair) = 407,556 number of mapped paired reads (singletons) = 3,118 number of mapped bases = 50,560,042 bp number of sequenced bases = 49,383,303 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,511 duplication rate = 51.12% >>>>>>> Insert size mean insert size = 1,310,978.2615 std insert size = 10,129,601.4046 median insert size = 145 >>>>>>> Mapping quality mean mapping quality = 41.8817 >>>>>>> ACTG content number of A's = 14,387,244 bp (29.13%) number of C's = 10,472,402 bp (21.21%) number of T's = 13,425,276 bp (27.19%) number of G's = 11,097,924 bp (22.47%) number of N's = 457 bp (0%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0392 number of mismatches = 1,887,782 number of insertions = 32,975 mapped reads with insertion percentage = 7.9% number of deletions = 159,793 mapped reads with deletion percentage = 37.51% homopolymer indels = 26.9% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 3.4175X 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 0.01% 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 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 1141382 0.0045792543882969905 1.6919189972967403 chr2 243199373 1721333 0.007077867754206752 2.3632306390772784 chr3 198022430 1046938 0.0052869667340209895 2.1604100029139732 chr4 191154276 1384151 0.007241015105516133 1.9507824041906325 chr5 180915260 1017991 0.0056268940497335605 2.130750830232497 chr6 171115067 1550445 0.00906083273193003 2.8171221821316754 chr7 159138663 1089868 0.006848543147556794 2.0393010604966384 chr8 146364022 888376 0.006069633697275687 1.4631233998228066 chr9 141213431 1152768 0.008163302823511171 3.3570542371057175 chr10 135534747 1148398 0.008473089192397282 2.507127744056649 chr11 135006516 1617114 0.0119780440819612 2.780947017587551 chr12 133851895 1659550 0.012398404968416772 3.461874795076521 chr13 115169878 1219158 0.010585736662845123 3.0342352790496525 chr14 107349540 199437 0.0018578281751370337 0.6661925288301728 chr15 102531392 576812 0.005625711196820579 1.33436637334017 chr16 90354753 189984 0.0021026453362115883 0.5842915051201562 chr17 81195210 521499 0.0064227803585950455 1.807995261270927 chr18 78077248 279462 0.003579301360621727 1.188487482892281 chr19 59128983 134006 0.0022663335846652395 0.6952455470148868 chr20 63025520 214726 0.0034069691134638795 0.9861742386621332 chr21 48129895 172619 0.0035865235110111916 1.0497400440501048 chr22 51304566 97364 0.0018977648110306594 0.7260805154381006 chrMT 16571 519667 31.360026552410837 182.99856290748298 chrX 155270560 30038738 0.19346061481326532 11.564755351324566 chrY 59373566 978256 0.016476288454697164 4.055588440588359