BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173954.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,885,884 number of mapped reads = 2,820,391 (97.73%) number of supplementary alignments = 362,614 (12.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,410,678 number of mapped paired reads (second in pair) = 1,409,713 number of mapped paired reads (both in pair) = 2,779,200 number of mapped paired reads (singletons) = 41,191 number of mapped bases = 321,172,822 bp number of sequenced bases = 320,972,096 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,250,170 duplication rate = 64.93% >>>>>>> Insert size mean insert size = 1,090,651.5939 std insert size = 9,964,332.1073 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.6119 >>>>>>> ACTG content number of A's = 95,365,888 bp (29.71%) number of C's = 64,205,577 bp (20%) number of T's = 94,547,543 bp (29.46%) number of G's = 66,850,726 bp (20.83%) number of N's = 2,362 bp (0%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,714,878 number of insertions = 34,377 mapped reads with insertion percentage = 1.17% number of deletions = 83,745 mapped reads with deletion percentage = 2.9% homopolymer indels = 41.72% >>>>>>> Coverage mean coverageData = 0.1037X std coverageData = 2.0092X There is a 2.27% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 1.28% of reference with a coverageData >= 3X There is a 1.03% of reference with a coverageData >= 4X There is a 0.77% of reference with a coverageData >= 5X There is a 0.63% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% 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% 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 27187851 0.10907836815379489 1.089301737491059 chr2 243199373 28841734 0.11859296199748015 6.209932095817329 chr3 198022430 21755912 0.10986589751474113 0.9910680328026071 chr4 191154276 20781673 0.10871675713913928 1.1473288662319532 chr5 180915260 18668326 0.10318823298819568 0.9484406250833549 chr6 171115067 18313356 0.10702363223222185 1.0292613050105355 chr7 159138663 18041865 0.11337197799632136 1.1427914778243762 chr8 146364022 16532536 0.11295491729518065 1.291933573065387 chr9 141213431 14075967 0.0996786700834427 1.078809559530806 chr10 135534747 15526108 0.11455444705998528 1.2926239823558925 chr11 135006516 14377320 0.10649352657911712 0.9705091481788373 chr12 133851895 14171454 0.10587413797914479 0.969471575689791 chr13 115169878 10176601 0.08836165477226605 0.8824635589931238 chr14 107349540 10059737 0.09371010811969945 0.9051019348197288 chr15 102531392 10524839 0.1026499181831063 0.9602040943903888 chr16 90354753 9301153 0.10294038433152487 0.9938268752811343 chr17 81195210 9087503 0.11192166385184545 0.9770132239185488 chr18 78077248 9861009 0.12629811183918777 1.3392445616007793 chr19 59128983 6629608 0.112121123409141 1.0233303222475316 chr20 63025520 7229556 0.11470839114060463 1.0171089747372406 chr21 48129895 4721746 0.09810422399633326 1.0594576614670523 chr22 51304566 4450390 0.08674452094575753 0.9706792518231396 chrMT 16571 483968 29.20572083760787 26.25071519706829 chrX 155270560 7799763 0.05023336684043646 0.659089573057145 chrY 59373566 2572847 0.043333206565359404 0.759231966648392