BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083634.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,417,483 number of mapped reads = 1,993,310 (82.45%) number of supplementary alignments = 13,012 (0.54%) number of secondary alignments = 0 number of mapped bases = 121,332,612 bp number of sequenced bases = 121,292,083 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,228 duplication rate = 2.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7505 >>>>>>> ACTG content number of A's = 36,028,024 bp (29.7%) number of C's = 23,524,811 bp (19.4%) number of T's = 35,779,046 bp (29.5%) number of G's = 25,943,608 bp (21.39%) number of N's = 16,594 bp (0.01%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,033,429 number of insertions = 8,675 mapped reads with insertion percentage = 0.43% number of deletions = 25,163 mapped reads with deletion percentage = 1.25% homopolymer indels = 45.53% >>>>>>> Coverage mean coverageData = 0.0392X std coverageData = 0.2994X There is a 3.47% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 8650597 0.03470642105240733 0.50135704253357 chr2 243199373 11220689 0.046137820429331455 0.2922565581816574 chr3 198022430 8987335 0.04538543941714077 0.2333327824613258 chr4 191154276 7394854 0.03868526592625111 0.22384411673284677 chr5 180915260 8136842 0.044975984889279105 0.2329377134564464 chr6 171115067 7985716 0.046668689905606034 0.2654800513861929 chr7 159138663 6946736 0.043652094777244674 0.4333645856358904 chr8 146364022 6403524 0.043750669819663746 0.40602545445759386 chr9 141213431 5243321 0.0371304695514409 0.2590986947874534 chr10 135534747 5817773 0.04292458671133241 0.3201260352568727 chr11 135006516 4845915 0.03589393418610995 0.22851910248912594 chr12 133851895 5292943 0.03954328028004385 0.2196844933929029 chr13 115169878 3725201 0.03234527173850093 0.19660666072426627 chr14 107349540 3429029 0.031942652013227074 0.19987994908141368 chr15 102531392 3646481 0.03556453227514945 0.2071624924146483 chr16 90354753 2911898 0.032227391513095054 0.2139961175091532 chr17 81195210 3467564 0.04270650941108472 0.2557834353494595 chr18 78077248 3249877 0.04162386717318725 0.42182473477789567 chr19 59128983 2097072 0.03546605900527665 0.3674208847070961 chr20 63025520 2400125 0.03808179607244811 0.21515107402905237 chr21 48129895 1440115 0.029921424096188035 0.1998138700082836 chr22 51304566 1315131 0.02563380031321189 0.17459542876365433 chrMT 16571 75191 4.537505280308974 3.3400241020015433 chrX 155270560 6338034 0.0408192898898542 0.2337854115351051 chrY 59373566 310649 0.005232109521600909 0.12462721576468372