BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536757.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 20,993,248 number of mapped reads = 20,519,507 (97.74%) number of supplementary alignments = 551 (0%) number of secondary alignments = 0 number of mapped bases = 1,023,562,850 bp number of sequenced bases = 1,023,473,668 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 216,578 duplication rate = 1.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4037 >>>>>>> ACTG content number of A's = 315,248,370 bp (30.8%) number of C's = 194,988,686 bp (19.05%) number of T's = 315,241,704 bp (30.8%) number of G's = 197,959,209 bp (19.34%) number of N's = 35,699 bp (0%) GC percentage = 38.39% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 1,930,096 number of insertions = 58,467 mapped reads with insertion percentage = 0.28% number of deletions = 53,530 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.8% >>>>>>> Coverage mean coverageData = 0.3306X std coverageData = 0.6785X There is a 24.41% of reference with a coverageData >= 1X There is a 6.37% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.01% 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 79238839 0.3179082911893728 0.6772687835316112 chr2 243199373 98293419 0.4041680609102557 0.7414913619540847 chr3 198022430 72725719 0.367260006858819 0.698326005349913 chr4 191154276 90671807 0.4743383663570257 0.7993645947746776 chr5 180915260 75600308 0.4178768999364675 0.7481383081440983 chr6 171115067 62675131 0.36627476527242336 0.7081218635523099 chr7 159138663 63055212 0.39622811208361103 0.741540493074638 chr8 146364022 55410379 0.37857923171857083 0.7097070079213208 chr9 141213431 41390102 0.2931031539060899 0.6450924783146536 chr10 135534747 38795893 0.2862431506217369 0.6135727283665373 chr11 135006516 49966974 0.3701078694601674 0.7187149452364577 chr12 133851895 51192789 0.3824584552949362 0.7301633490395678 chr13 115169878 41003594 0.35602706811932194 0.7014368793315274 chr14 107349540 33576900 0.31278103287634024 0.6632061000327484 chr15 102531392 28384686 0.27683898020227793 0.6290800780989845 chr16 90354753 17786857 0.19685579794568195 0.5177171424911772 chr17 81195210 17189149 0.21170151539727528 0.544618021955788 chr18 78077248 28527151 0.36537085682118303 0.6962732059272198 chr19 59128983 8371273 0.14157647527947503 0.43097649474726635 chr20 63025520 14873335 0.2359890882296568 0.5644438244524116 chr21 48129895 10556543 0.21933442821763896 0.5545409486810488 chr22 51304566 5629774 0.109732416409097 0.38190677207148416 chrMT 16571 1288 0.0777261480900368 0.2970180202929376 chrX 155270560 34658628 0.22321442004202213 0.5421993098514802 chrY 59373566 3987100 0.06715277974039828 0.3031158740949724