BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716565.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 = 1,232,734 number of mapped reads = 1,135,571 (92.12%) number of supplementary alignments = 27,360 (2.22%) number of secondary alignments = 0 number of mapped bases = 86,853,225 bp number of sequenced bases = 86,817,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,383 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4449 >>>>>>> ACTG content number of A's = 22,433,090 bp (25.84%) number of C's = 17,299,531 bp (19.93%) number of T's = 25,532,439 bp (29.41%) number of G's = 21,548,953 bp (24.82%) number of N's = 3,414 bp (0%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 571,679 number of insertions = 7,615 mapped reads with insertion percentage = 0.66% number of deletions = 17,123 mapped reads with deletion percentage = 1.48% homopolymer indels = 37.67% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.2374X There is a 2.47% of reference with a coverageData >= 1X There is a 0.24% 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 0.01% 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 7115309 0.028546805506253884 0.3058256070518373 chr2 243199373 7234403 0.0297467995528097 0.26794648661052883 chr3 198022430 5688724 0.028727674940662026 0.1871576694412017 chr4 191154276 5497890 0.02876153290967972 0.26012590517914747 chr5 180915260 5096528 0.02817080217555998 0.1845877700251115 chr6 171115067 4920030 0.028752757347779316 0.1957376217659805 chr7 159138663 4729768 0.029721048994863053 0.2796439547272489 chr8 146364022 4351484 0.029730557691288368 0.24058348617410547 chr9 141213431 3640344 0.025779020977119378 0.22025302450766215 chr10 135534747 4290922 0.031659202492184534 0.3275966355513843 chr11 135006516 3966688 0.02938145592913456 0.24649363286786738 chr12 133851895 3910962 0.029218577742212766 0.19026931830833066 chr13 115169878 2550784 0.02214801338940378 0.16437495491957374 chr14 107349540 2606018 0.02427600528143856 0.1863077093335614 chr15 102531392 2547383 0.024844907986814418 0.1739832673687461 chr16 90354753 2742868 0.030356654286908404 0.20601447369716067 chr17 81195210 2500014 0.03079016607014133 0.21362268152717437 chr18 78077248 2301864 0.02948187927935165 0.3181711356684165 chr19 59128983 1932743 0.03268689738837551 0.2736450250322323 chr20 63025520 1889538 0.029980522175778953 0.20437930129040233 chr21 48129895 1173129 0.02437422728638822 0.2219569713423493 chr22 51304566 1173773 0.022878528979272526 0.1713033529060107 chrMT 16571 13125 0.7920463460261903 1.1294182333322158 chrX 155270560 4663216 0.030032840739416408 0.2050154332750904 chrY 59373566 315718 0.005317484215113507 0.21794890813103415