BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524593.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 = 2,285,006 number of mapped reads = 2,123,321 (92.92%) number of supplementary alignments = 4,726 (0.21%) number of secondary alignments = 0 number of mapped bases = 123,761,225 bp number of sequenced bases = 123,721,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 125,312 duplication rate = 4.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3365 >>>>>>> ACTG content number of A's = 32,738,738 bp (26.46%) number of C's = 22,781,706 bp (18.41%) number of T's = 37,926,411 bp (30.65%) number of G's = 30,273,988 bp (24.47%) number of N's = 904 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 590,926 number of insertions = 9,335 mapped reads with insertion percentage = 0.44% number of deletions = 23,171 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.95% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.346X There is a 3.39% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.08% 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 0.01% 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 12695108 0.050933104796557355 0.6393052898042617 chr2 243199373 10942036 0.04499204033720926 0.4077158571065357 chr3 198022430 7927595 0.0400338234411122 0.23259674316211687 chr4 191154276 5582893 0.029206215611938494 0.23346328276167044 chr5 180915260 7712335 0.04262954379857177 0.23787954309276513 chr6 171115067 8087323 0.04726248332065346 0.2744380700148461 chr7 159138663 7571905 0.0475805492974388 0.45206102949742 chr8 146364022 11087843 0.07575524946970916 0.4583417687288756 chr9 141213431 4421923 0.031313756550536614 0.30605112423596886 chr10 135534747 5328432 0.03931413986407486 0.34023497840644457 chr11 135006516 6327976 0.046871633958763884 0.32093305082648194 chr12 133851895 3814283 0.02849629435578779 0.20261402467027997 chr13 115169878 3092449 0.02685119628241683 0.19276976284046743 chr14 107349540 2258472 0.021038487915271922 0.17590544770382952 chr15 102531392 3195100 0.031162163486476414 0.21087770645218912 chr16 90354753 3643519 0.0403245969805263 0.24798157887233152 chr17 81195210 2708590 0.033358987556039325 0.21986507786884268 chr18 78077248 3327983 0.0426242354238715 0.5086054294634882 chr19 59128983 2401987 0.04062283635082985 0.4279022407236022 chr20 63025520 2280164 0.03617842423196191 0.22130828126915175 chr21 48129895 1098238 0.02281820893230704 0.19936606813210148 chr22 51304566 2296982 0.044771492658177835 0.245097248578017 chrMT 16571 6652 0.4014241747631404 0.6751152632138432 chrX 155270560 5651793 0.03639964330649674 0.25549322357121346 chrY 59373566 299644 0.0050467576766401396 0.13972274731330736