BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472463.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,370,364 number of mapped reads = 17,242,538 (99.26%) number of supplementary alignments = 57,659 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,640,101 number of mapped paired reads (second in pair) = 8,602,437 number of mapped paired reads (both in pair) = 17,164,626 number of mapped paired reads (singletons) = 77,912 number of mapped bases = 1,693,745,400 bp number of sequenced bases = 1,693,541,368 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,915,922 duplication rate = 48.19% >>>>>>> Insert size mean insert size = 16,520.9423 std insert size = 1,285,877.7217 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 55.1661 >>>>>>> ACTG content number of A's = 468,507,692 bp (27.66%) number of C's = 378,998,023 bp (22.38%) number of T's = 469,762,864 bp (27.74%) number of G's = 376,061,473 bp (22.21%) number of N's = 211,316 bp (0.01%) GC percentage = 44.58% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 8,859,617 number of insertions = 93,515 mapped reads with insertion percentage = 0.54% number of deletions = 86,918 mapped reads with deletion percentage = 0.49% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.5471X std coverageData = 17.2017X There is a 4.74% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 228278065 0.9158575576828754 26.261661224808886 chr2 243199373 129301318 0.5316679743249174 16.177478808841464 chr3 198022430 168261093 0.8497072427603277 16.75875171594692 chr4 191154276 71199795 0.37247293908298446 13.513031867237071 chr5 180915260 108742134 0.60106667618862 18.981303157644255 chr6 171115067 142669391 0.8337628795715576 23.83096807434012 chr7 159138663 68439059 0.4300592810686112 11.822430210982166 chr8 146364022 93001026 0.6354090624812155 16.814531442863192 chr9 141213431 76675319 0.5429746905590022 13.226114112733844 chr10 135534747 35883689 0.2647563801480369 8.410661446796778 chr11 135006516 70196400 0.5199482371650862 18.064785308010578 chr12 133851895 96143871 0.7182854676805286 24.432742962315622 chr13 115169878 40057196 0.34780965904991235 11.399289969899874 chr14 107349540 46168085 0.4300724996120151 14.46789282178087 chr15 102531392 34410319 0.33560764492498063 11.901076521898691 chr16 90354753 92708194 1.026046676260628 31.899849011060564 chr17 81195210 49949090 0.6151728654929275 14.861659085381254 chr18 78077248 25297032 0.3240000467229583 9.331579097449154 chr19 59128983 22157394 0.3747298342675706 11.168156319998696 chr20 63025520 21156804 0.3356863061185374 13.002013944604808 chr21 48129895 8249618 0.17140319961221606 8.181361747230424 chr22 51304566 9422805 0.18366406218113218 4.61718724442905 chrMT 16571 3461 0.2088588497978396 0.5744543041074733 chrX 155270560 54001776 0.34779146800269156 9.676130602544406 chrY 59373566 1372466 0.023115775124573114 0.5632593680456984