BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867866.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 22,597,829 number of mapped reads = 20,266,524 (89.68%) number of supplementary alignments = 77,148 (0.34%) number of secondary alignments = 0 number of mapped bases = 1,810,805,293 bp number of sequenced bases = 1,810,344,432 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,028,396 duplication rate = 1.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.4779 >>>>>>> ACTG content number of A's = 511,068,854 bp (28.23%) number of C's = 390,731,630 bp (21.58%) number of T's = 511,708,581 bp (28.27%) number of G's = 396,780,559 bp (21.92%) number of N's = 54,808 bp (0%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 8,540,197 number of insertions = 171,963 mapped reads with insertion percentage = 0.83% number of deletions = 181,157 mapped reads with deletion percentage = 0.87% homopolymer indels = 36.1% >>>>>>> Coverage mean coverageData = 0.5849X std coverageData = 6.1657X There is a 40.05% of reference with a coverageData >= 1X There is a 11.89% of reference with a coverageData >= 2X There is a 2.91% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 184330400 0.7395383781210318 12.010777909103648 chr2 243199373 151278484 0.6220348438151606 3.8442412612625425 chr3 198022430 115209514 0.5818003243369956 3.6665824812465715 chr4 191154276 113705350 0.5948355034443488 4.114709149913157 chr5 180915260 95460482 0.5276530127972621 0.9323872776995593 chr6 171115067 95161177 0.556123891766936 1.7924214735843709 chr7 159138663 92765860 0.5829247164153943 2.6702795015849503 chr8 146364022 102348160 0.6992713004292818 2.7121469432227148 chr9 141213431 70641186 0.5002441021350158 3.478637965709225 chr10 135534747 102059027 0.7530100528390701 19.477507655202835 chr11 135006516 76738086 0.5684028317566538 2.257189648943149 chr12 133851895 79538995 0.5942313704262461 0.9990082327957582 chr13 115169878 39616018 0.34397898728346316 0.6547388591122721 chr14 107349540 46781712 0.43578865824669577 1.030658905324714 chr15 102531392 52197742 0.5090903476664006 0.802913943015854 chr16 90354753 65268442 0.7223575941821234 6.409296965460261 chr17 81195210 48900015 0.6022524604591822 1.6606342898570816 chr18 78077248 48334451 0.6190593577273625 7.565072847299973 chr19 59128983 36799412 0.622358277327381 7.058871145857616 chr20 63025520 41390060 0.6567190560268285 1.4895703019827915 chr21 48129895 24948861 0.5183651657665158 3.026064148049838 chr22 51304566 26207543 0.5108228183822859 0.8905340060835532 chrMT 16571 2847657 171.84581497797356 54.20050734872383 chrX 155270560 89697270 0.5776836896833502 1.6805810575904132 chrY 59373566 8579389 0.14449846249760373 6.025474478963456