BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008698.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,650,083 number of mapped reads = 1,472,240 (89.22%) number of supplementary alignments = 15,463 (0.94%) number of secondary alignments = 0 number of mapped bases = 95,716,274 bp number of sequenced bases = 95,658,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,727 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2782 >>>>>>> ACTG content number of A's = 25,560,709 bp (26.72%) number of C's = 17,962,053 bp (18.78%) number of T's = 29,920,948 bp (31.28%) number of G's = 22,151,889 bp (23.16%) number of N's = 63,015 bp (0.07%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 830,527 number of insertions = 7,247 mapped reads with insertion percentage = 0.49% number of deletions = 34,427 mapped reads with deletion percentage = 2.31% homopolymer indels = 44.72% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.2927X There is a 2.64% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% 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 8389106 0.03365731233223287 0.5280424511742517 chr2 243199373 9021112 0.03709348378953263 0.3798078003109212 chr3 198022430 7013434 0.035417371658352036 0.21267921094483475 chr4 191154276 5098291 0.026671080065192997 0.19724801654602953 chr5 180915260 4040244 0.022332245494382286 0.17037604143803584 chr6 171115067 4897798 0.028622833078749285 0.21505558207302847 chr7 159138663 5357685 0.0336667714746353 0.3234437158110372 chr8 146364022 7381269 0.05043089756033078 0.33506131856363575 chr9 141213431 3005292 0.02128191333301717 0.25294046506130263 chr10 135534747 5838733 0.04307923340130631 0.3020577859342273 chr11 135006516 4496883 0.033308636747577426 0.3219519190197303 chr12 133851895 4213212 0.03147667053947947 0.2031924454876215 chr13 115169878 2090622 0.018152506856002747 0.15082793499716646 chr14 107349540 3792300 0.03532665347238563 0.2166600928184505 chr15 102531392 2450836 0.02390327442350534 0.1776907465087022 chr16 90354753 2961397 0.03277522102240709 0.21697649319550638 chr17 81195210 2627657 0.03236221693373292 0.2521997372133812 chr18 78077248 1498155 0.019188112265432305 0.4201766275216702 chr19 59128983 2168122 0.036667669389815145 0.373308613914723 chr20 63025520 2562318 0.04065524568460522 0.2329781344963559 chr21 48129895 1111765 0.023099260864791 0.18325389662159874 chr22 51304566 1337937 0.026078322151677494 0.18217617625329396 chrMT 16571 42849 2.585782390923903 2.6523626474004605 chrX 155270560 4052168 0.02609746496695832 0.20325595935609564 chrY 59373566 267089 0.004498449697294584 0.14151980416768561