BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084894.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 = 2,797,730 number of mapped reads = 2,535,250 (90.62%) number of supplementary alignments = 17,046 (0.61%) number of secondary alignments = 0 number of mapped bases = 173,051,392 bp number of sequenced bases = 172,986,237 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,652 duplication rate = 3.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3141 >>>>>>> ACTG content number of A's = 49,355,357 bp (28.53%) number of C's = 31,689,365 bp (18.32%) number of T's = 54,938,350 bp (31.76%) number of G's = 36,976,059 bp (21.38%) number of N's = 27,106 bp (0.02%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,431,200 number of insertions = 13,352 mapped reads with insertion percentage = 0.52% number of deletions = 37,047 mapped reads with deletion percentage = 1.45% homopolymer indels = 48.97% >>>>>>> Coverage mean coverageData = 0.0559X std coverageData = 0.4002X There is a 4.77% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 14367190 0.05764154144273927 0.6811704039059702 chr2 243199373 14737318 0.0605976808994487 0.5242516628338081 chr3 198022430 13302085 0.0671746377417952 0.2926545875610244 chr4 191154276 9485546 0.04962246306224403 0.252609969488901 chr5 180915260 8731842 0.04826481746205378 0.25200504851085287 chr6 171115067 10907626 0.0637443925379172 0.2937875554748286 chr7 159138663 10874821 0.06833550562128325 0.46504748493792664 chr8 146364022 9908411 0.06769703964543965 0.4932255161597099 chr9 141213431 13489204 0.0955235199971878 0.49757944753472744 chr10 135534747 5512099 0.04066926837588002 0.326829883893195 chr11 135006516 6813894 0.050470852829059006 0.32627829633122296 chr12 133851895 7101742 0.0530567161563159 0.2668830591828869 chr13 115169878 4204308 0.036505274408643554 0.21298397222501467 chr14 107349540 3670678 0.03419370031767253 0.22849645043492955 chr15 102531392 4745643 0.04628478076255904 0.24073319610420052 chr16 90354753 3312742 0.03666372703160397 0.23532756995046497 chr17 81195210 3747617 0.04615564144732183 0.2515823901642997 chr18 78077248 6728814 0.08618149553631808 0.6832674684969753 chr19 59128983 3360084 0.05682634521212719 0.4432916567704376 chr20 63025520 3316141 0.05261584513701751 0.26087496349710243 chr21 48129895 1499970 0.031165037862642336 0.20868111990017754 chr22 51304566 1599140 0.03116954541628907 0.19390255589815625 chrMT 16571 392865 23.707983827167944 11.7009033191792 chrX 155270560 10897688 0.0701851529356241 0.33980216467862356 chrY 59373566 343924 0.005792544109612685 0.11789974346652941