BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708589.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,752,197 number of mapped reads = 4,646,477 (97.78%) number of supplementary alignments = 109 (0%) number of secondary alignments = 0 number of mapped bases = 231,760,450 bp number of sequenced bases = 231,740,291 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,723 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.59 >>>>>>> ACTG content number of A's = 71,872,881 bp (31.01%) number of C's = 43,862,770 bp (18.93%) number of T's = 71,519,039 bp (30.86%) number of G's = 44,477,375 bp (19.19%) number of N's = 8,226 bp (0%) GC percentage = 38.12% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 341,970 number of insertions = 14,529 mapped reads with insertion percentage = 0.31% number of deletions = 11,753 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.86% >>>>>>> Coverage mean coverageData = 0.0749X std coverageData = 0.2892X There is a 6.84% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.05% 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 19452755 0.07804496101937496 0.296185374374045 chr2 243199373 16160457 0.0664494188478027 0.2693331878773872 chr3 198022430 15534739 0.07844939080890988 0.29370830557842287 chr4 191154276 18056765 0.09446173728282176 0.32390589736400804 chr5 180915260 16043921 0.08868196635264487 0.31228875801727923 chr6 171115067 13614224 0.07956180737725452 0.29732449533427774 chr7 159138663 13826236 0.08688169008935308 0.3114271265059724 chr8 146364022 14822887 0.10127411639453308 0.33625652146549223 chr9 141213431 9710635 0.06876566153257758 0.2779797178416762 chr10 135534747 8267178 0.06099674203840879 0.2578223897844633 chr11 135006516 15787663 0.11694000754748755 0.364356059527664 chr12 133851895 12030673 0.08988048320122774 0.31731617024962716 chr13 115169878 8554117 0.07427390866907058 0.2884642279465613 chr14 107349540 5901048 0.054970407884374725 0.24707518784818916 chr15 102531392 5460641 0.05325823529246536 0.24403862006973542 chr16 90354753 4521732 0.05004420741430171 0.23466541561142976 chr17 81195210 3927650 0.048372927417762696 0.23211249782857626 chr18 78077248 6699834 0.08581032466718089 0.3076226236013177 chr19 59128983 1788664 0.030250207415202793 0.1801526711420552 chr20 63025520 4128520 0.0655055285541476 0.2699312301940953 chr21 48129895 2578009 0.053563570001555164 0.2461297989870877 chr22 51304566 1252038 0.024404026729316842 0.16372456768163232 chrMT 16571 295 0.017802184539255327 0.13223186743325388 chrX 155270560 13343548 0.08593739856415794 0.30757563195861287 chrY 59373566 296221 0.004989105757939484 0.07454269828776745