BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524394.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 = 3,780,831 number of mapped reads = 3,471,158 (91.81%) number of supplementary alignments = 11,785 (0.31%) number of secondary alignments = 0 number of mapped bases = 202,629,412 bp number of sequenced bases = 202,571,641 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 217,032 duplication rate = 4.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4968 >>>>>>> ACTG content number of A's = 48,761,164 bp (24.07%) number of C's = 36,012,833 bp (17.78%) number of T's = 66,422,286 bp (32.79%) number of G's = 51,349,753 bp (25.35%) number of N's = 25,605 bp (0.01%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 989,052 number of insertions = 14,182 mapped reads with insertion percentage = 0.41% number of deletions = 36,286 mapped reads with deletion percentage = 1.04% homopolymer indels = 44.21% >>>>>>> Coverage mean coverageData = 0.0655X std coverageData = 0.602X There is a 5.37% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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% 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 17536159 0.07035552782032989 1.3922913658713374 chr2 243199373 16152699 0.06641751909450852 0.6794083386929906 chr3 198022430 14189956 0.07165832678651606 0.3146957884546426 chr4 191154276 13252050 0.06932646382443466 0.3825654888556424 chr5 180915260 13115328 0.0724943158470988 0.3182536310865684 chr6 171115067 7945550 0.04643395896867457 0.3037623903909581 chr7 159138663 11261127 0.07076298611356312 0.86591477440636 chr8 146364022 11033030 0.0753807516986654 0.49938188175896475 chr9 141213431 6910859 0.04893910551610349 0.4084505085778153 chr10 135534747 10239284 0.07554729858314488 0.5209334418311694 chr11 135006516 7523367 0.05572595473836241 0.4313595026990167 chr12 133851895 9257008 0.06915858755679179 0.3253143517269455 chr13 115169878 6769180 0.05877561144937568 0.28536485797155586 chr14 107349540 5603622 0.05219977654305738 0.29000267533144114 chr15 102531392 6380695 0.062231623657269766 0.2946503800986121 chr16 90354753 6060991 0.0670799354628306 0.33632218018772897 chr17 81195210 5316392 0.0654766703602343 0.3456274695590706 chr18 78077248 5918660 0.07580518206789255 0.7783997851564813 chr19 59128983 5723116 0.09679036759350318 0.9042328390243765 chr20 63025520 5886450 0.09339788073148782 0.3952764238558842 chr21 48129895 2798127 0.058136985339361326 0.34179592431282324 chr22 51304566 1402227 0.027331426992287588 0.19245727050297937 chrMT 16571 20666 1.2471184599601715 1.451788825469861 chrX 155270560 11707629 0.07540147340229854 0.3956255895254488 chrY 59373566 625240 0.010530612225649374 0.26618680987164767