BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716431.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 = 1,585,101 number of mapped reads = 1,414,101 (89.21%) number of supplementary alignments = 30,562 (1.93%) number of secondary alignments = 0 number of mapped bases = 104,782,289 bp number of sequenced bases = 104,746,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,814 duplication rate = 1.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1983 >>>>>>> ACTG content number of A's = 27,351,531 bp (26.11%) number of C's = 22,332,448 bp (21.32%) number of T's = 31,148,205 bp (29.74%) number of G's = 23,901,793 bp (22.82%) number of N's = 12,045 bp (0.01%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 764,430 number of insertions = 9,224 mapped reads with insertion percentage = 0.64% number of deletions = 21,221 mapped reads with deletion percentage = 1.48% homopolymer indels = 40.3% >>>>>>> Coverage mean coverageData = 0.0338X std coverageData = 0.2697X There is a 2.99% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 8380099 0.0336211760130379 0.31682785900927113 chr2 243199373 8931365 0.03672445734471528 0.36504805896633996 chr3 198022430 6932669 0.03500951382123732 0.20561682269009984 chr4 191154276 6670720 0.034897048287844734 0.2188200800691298 chr5 180915260 6369155 0.035205183907648256 0.20813834168897216 chr6 171115067 6069564 0.0354706578819269 0.22593564396166627 chr7 159138663 5768196 0.03624635202571735 0.3289789444360361 chr8 146364022 5342037 0.036498293275925416 0.32275675660126335 chr9 141213431 4377552 0.030999544228905534 0.27756940172223643 chr10 135534747 4962102 0.03661129053496518 0.2755975431158963 chr11 135006516 4726341 0.0350082436021088 0.2990505731650086 chr12 133851895 4750898 0.03549369248750643 0.20951060913500644 chr13 115169878 3358475 0.029161053726218238 0.18742229371132085 chr14 107349540 3160256 0.029438933785836438 0.21853984536135743 chr15 102531392 3005889 0.029316767688085225 0.18952079283772574 chr16 90354753 3110819 0.034428946975263164 0.2204185388379677 chr17 81195210 2927678 0.03605727480722077 0.22511920264440693 chr18 78077248 2849468 0.03649549738228479 0.4880119339671917 chr19 59128983 2137915 0.03615680317045196 0.2878428664523495 chr20 63025520 2226059 0.035319962453304626 0.21542815460028508 chr21 48129895 1388605 0.0288511952914088 0.1973459308799702 chr22 51304566 1192973 0.023252764675954964 0.16835844235998199 chrMT 16571 4457 0.2689638525134271 0.5716022320301051 chrX 155270560 5876432 0.03784640179052616 0.2524521724417775 chrY 59373566 262565 0.004422254172841833 0.12613047336133779