BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714166.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 816,878 number of mapped reads = 753,222 (92.21%) number of supplementary alignments = 31,325 (3.83%) number of secondary alignments = 0 number of mapped bases = 96,316,294 bp number of sequenced bases = 94,444,814 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 728,021 duplication rate = 39.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7949 >>>>>>> ACTG content number of A's = 25,463,857 bp (26.96%) number of C's = 20,525,114 bp (21.73%) number of T's = 24,251,877 bp (25.68%) number of G's = 24,203,339 bp (25.63%) number of N's = 627 bp (0%) GC percentage = 47.36% >>>>>>> Mismatches and indels general error rate = 0.0425 number of mismatches = 3,639,932 number of insertions = 143,943 mapped reads with insertion percentage = 18.68% number of deletions = 304,937 mapped reads with deletion percentage = 38.63% homopolymer indels = 28.18% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 14.6176X There is a 0.04% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% 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% 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 8304995 0.03331985680388736 17.39813961471212 chr2 243199373 13093774 0.053839670055399365 20.668375936691252 chr3 198022430 3023768 0.015269825746507605 5.373575405493313 chr4 191154276 5294339 0.027696680978248168 18.8073432160316 chr5 180915260 7734680 0.04275305466216614 17.576962943083043 chr6 171115067 3814657 0.022292934613408415 7.6857186386770255 chr7 159138663 1819365 0.011432576884223288 2.758109365001541 chr8 146364022 7851452 0.05364331953107984 25.699619820363655 chr9 141213431 1693800 0.01199460977617632 2.9148292102280275 chr10 135534747 2970656 0.021918039954728363 6.9988632016422345 chr11 135006516 3703109 0.027429113125176863 6.644715163214403 chr12 133851895 6351466 0.047451446242132024 18.884482353131844 chr13 115169878 569811 0.0049475697108926344 1.8081029661685588 chr14 107349540 1484513 0.013828778399981966 3.414303351030115 chr15 102531392 1979186 0.01930321983729627 6.723378143972036 chr16 90354753 6111008 0.06763349793009782 22.085189814322597 chr17 81195210 4638523 0.05712803747905819 15.409576222036582 chr18 78077248 6260198 0.08017954218878207 34.84262913472264 chr19 59128983 1214661 0.020542565394706686 4.047403579467684 chr20 63025520 1621720 0.025731164137955547 7.257892863555868 chr21 48129895 153493 0.0031891405539114515 0.9007531233797139 chr22 51304566 219155 0.004271647088877041 1.027624581949303 chrMT 16571 23859 1.4398044777020096 11.197154838735301 chrX 155270560 6250318 0.040254366313871734 9.684349709977125 chrY 59373566 133788 0.0022533260003281593 0.8050564052124253