BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365356.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 568,335,354 number of mapped reads = 534,860,976 (94.11%) number of supplementary alignments = 2,501,403 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 268,042,799 number of mapped paired reads (second in pair) = 266,818,177 number of mapped paired reads (both in pair) = 532,063,754 number of mapped paired reads (singletons) = 2,797,222 number of mapped bases = 55,659,310,440 bp number of sequenced bases = 55,639,714,027 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 327,401,715 duplication rate = 31.14% >>>>>>> Insert size mean insert size = 51,887.4735 std insert size = 2,190,045.7847 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 53.7207 >>>>>>> ACTG content number of A's = 16,851,699,432 bp (30.29%) number of C's = 10,795,479,245 bp (19.4%) number of T's = 16,386,042,054 bp (29.45%) number of G's = 11,597,053,974 bp (20.84%) number of N's = 9,439,322 bp (0.02%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 331,903,431 number of insertions = 16,928,085 mapped reads with insertion percentage = 3.09% number of deletions = 9,163,568 mapped reads with deletion percentage = 1.67% homopolymer indels = 49.66% >>>>>>> Coverage mean coverageData = 17.9796X std coverageData = 228.4189X There is a 80.79% of reference with a coverageData >= 1X There is a 78.21% of reference with a coverageData >= 2X There is a 74.8% of reference with a coverageData >= 3X There is a 72.17% of reference with a coverageData >= 4X There is a 69.01% of reference with a coverageData >= 5X There is a 66.38% of reference with a coverageData >= 6X There is a 63.39% of reference with a coverageData >= 7X There is a 60.82% of reference with a coverageData >= 8X There is a 58.01% of reference with a coverageData >= 9X There is a 55.53% of reference with a coverageData >= 10X There is a 52.89% of reference with a coverageData >= 11X There is a 50.53% of reference with a coverageData >= 12X There is a 48.06% of reference with a coverageData >= 13X There is a 45.83% of reference with a coverageData >= 14X There is a 43.53% of reference with a coverageData >= 15X There is a 41.45% of reference with a coverageData >= 16X There is a 39.32% of reference with a coverageData >= 17X There is a 37.39% of reference with a coverageData >= 18X There is a 35.43% of reference with a coverageData >= 19X There is a 33.65% of reference with a coverageData >= 20X There is a 31.86% of reference with a coverageData >= 21X There is a 30.23% of reference with a coverageData >= 22X There is a 28.61% of reference with a coverageData >= 23X There is a 27.13% of reference with a coverageData >= 24X There is a 25.66% of reference with a coverageData >= 25X There is a 24.32% of reference with a coverageData >= 26X There is a 23% of reference with a coverageData >= 27X There is a 21.79% of reference with a coverageData >= 28X There is a 20.6% of reference with a coverageData >= 29X There is a 19.51% of reference with a coverageData >= 30X There is a 18.44% of reference with a coverageData >= 31X There is a 17.46% of reference with a coverageData >= 32X There is a 16.51% of reference with a coverageData >= 33X There is a 15.63% of reference with a coverageData >= 34X There is a 14.77% of reference with a coverageData >= 35X There is a 13.98% of reference with a coverageData >= 36X There is a 13.22% of reference with a coverageData >= 37X There is a 12.51% of reference with a coverageData >= 38X There is a 11.83% of reference with a coverageData >= 39X There is a 11.19% of reference with a coverageData >= 40X There is a 10.58% of reference with a coverageData >= 41X There is a 10.01% of reference with a coverageData >= 42X There is a 9.46% of reference with a coverageData >= 43X There is a 8.95% of reference with a coverageData >= 44X There is a 8.46% of reference with a coverageData >= 45X There is a 8.01% of reference with a coverageData >= 46X There is a 7.57% of reference with a coverageData >= 47X There is a 7.16% of reference with a coverageData >= 48X There is a 6.77% of reference with a coverageData >= 49X There is a 6.4% of reference with a coverageData >= 50X There is a 6.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4577543127 18.36522255645654 603.0991230186729 chr2 243199373 4878192370 20.05840849762388 133.64962706184204 chr3 198022430 3773507178 19.05595834774879 38.96879353592332 chr4 191154276 3901937703 20.41250546234184 127.00514758397085 chr5 180915260 3484270816 19.25913168408237 24.147012569328087 chr6 171115067 3319677853 19.40026621384545 80.82253458741386 chr7 159138663 3059673707 19.22646357158348 167.24909630051874 chr8 146364022 2870479535 19.611920305114328 71.84814732749217 chr9 141213431 2362252237 16.728240509927133 198.63288815706304 chr10 135534747 3004593095 22.16843401050507 498.60620451808194 chr11 135006516 2561915733 18.976237658040148 123.54447146579616 chr12 133851895 2466111649 18.42418180930498 37.490594609116464 chr13 115169878 1883727914 16.35608152680339 19.395682447838137 chr14 107349540 1686568672 15.711000457011739 25.61942683084767 chr15 102531392 1525338218 14.876792251099058 23.15014604061524 chr16 90354753 1569380327 17.36909542545039 77.14350670075969 chr17 81195210 1434934826 17.67265367008719 101.54105126252203 chr18 78077248 1586467989 20.319209880450703 230.92834823619498 chr19 59128983 1002140236 16.948375993546176 295.55025914158006 chr20 63025520 1102556482 17.49381015817085 39.984176643291725 chr21 48129895 792241661 16.460490117420782 71.82544753160172 chr22 51304566 610447669 11.898505661269994 54.20471683093392 chrMT 16571 49543216 2989.7541488141933 606.5153595261424 chrX 155270560 1550640546 9.986700286261607 49.77799263276755 chrY 59373566 605167681 10.192543951293072 234.01579449525158