BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432716.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 412,014,350 number of mapped reads = 411,856,618 (99.96%) number of supplementary alignments = 197,495 (0.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 205,932,948 number of mapped paired reads (second in pair) = 205,923,670 number of mapped paired reads (both in pair) = 411,797,230 number of mapped paired reads (singletons) = 59,388 number of mapped bases = 56,411,433,094 bp number of sequenced bases = 56,357,769,876 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 197,565,973 duplication rate = 32.07% >>>>>>> Insert size mean insert size = 71,909.1274 std insert size = 2,693,953.3197 median insert size = 305 >>>>>>> Mapping quality mean mapping quality = 55.4097 >>>>>>> ACTG content number of A's = 15,526,954,655 bp (27.55%) number of C's = 12,081,993,519 bp (21.44%) number of T's = 15,338,554,587 bp (27.22%) number of G's = 13,409,359,489 bp (23.79%) number of N's = 907,626 bp (0%) GC percentage = 45.23% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 512,185,063 number of insertions = 11,439,638 mapped reads with insertion percentage = 2.71% number of deletions = 36,785,908 mapped reads with deletion percentage = 8.53% homopolymer indels = 51.47% >>>>>>> Coverage mean coverageData = 18.2225X std coverageData = 49.8692X There is a 66.88% of reference with a coverageData >= 1X There is a 57.9% of reference with a coverageData >= 2X There is a 51.73% of reference with a coverageData >= 3X There is a 47.05% of reference with a coverageData >= 4X There is a 43.3% of reference with a coverageData >= 5X There is a 40.18% of reference with a coverageData >= 6X There is a 37.53% of reference with a coverageData >= 7X There is a 35.24% of reference with a coverageData >= 8X There is a 33.24% of reference with a coverageData >= 9X There is a 31.46% of reference with a coverageData >= 10X There is a 29.87% of reference with a coverageData >= 11X There is a 28.43% of reference with a coverageData >= 12X There is a 27.13% of reference with a coverageData >= 13X There is a 25.94% of reference with a coverageData >= 14X There is a 24.85% of reference with a coverageData >= 15X There is a 23.85% of reference with a coverageData >= 16X There is a 22.92% of reference with a coverageData >= 17X There is a 22.06% of reference with a coverageData >= 18X There is a 21.25% of reference with a coverageData >= 19X There is a 20.5% of reference with a coverageData >= 20X There is a 19.8% of reference with a coverageData >= 21X There is a 19.14% of reference with a coverageData >= 22X There is a 18.52% of reference with a coverageData >= 23X There is a 17.94% of reference with a coverageData >= 24X There is a 17.38% of reference with a coverageData >= 25X There is a 16.86% of reference with a coverageData >= 26X There is a 16.36% of reference with a coverageData >= 27X There is a 15.89% of reference with a coverageData >= 28X There is a 15.45% of reference with a coverageData >= 29X There is a 15.02% of reference with a coverageData >= 30X There is a 14.61% of reference with a coverageData >= 31X There is a 14.23% of reference with a coverageData >= 32X There is a 13.86% of reference with a coverageData >= 33X There is a 13.5% of reference with a coverageData >= 34X There is a 13.16% of reference with a coverageData >= 35X There is a 12.84% of reference with a coverageData >= 36X There is a 12.53% of reference with a coverageData >= 37X There is a 12.23% of reference with a coverageData >= 38X There is a 11.94% of reference with a coverageData >= 39X There is a 11.66% of reference with a coverageData >= 40X There is a 11.4% of reference with a coverageData >= 41X There is a 11.14% of reference with a coverageData >= 42X There is a 10.89% of reference with a coverageData >= 43X There is a 10.66% of reference with a coverageData >= 44X There is a 10.43% of reference with a coverageData >= 45X There is a 10.21% of reference with a coverageData >= 46X There is a 9.99% of reference with a coverageData >= 47X There is a 9.79% of reference with a coverageData >= 48X There is a 9.59% of reference with a coverageData >= 49X There is a 9.39% of reference with a coverageData >= 50X There is a 9.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4862562003 19.50872572951383 52.09715080733912 chr2 243199373 4617675947 18.987203338719134 53.845926921009 chr3 198022430 3772650766 19.05163352454568 47.12844366303694 chr4 191154276 2615516394 13.682751172147464 38.41294462097955 chr5 180915260 3230171271 17.85460922975762 46.49302360534956 chr6 171115067 2837443987 16.582081500748266 43.27483315360876 chr7 159138663 3713620044 23.33574993023537 58.14153989338818 chr8 146364022 3663353593 25.029057981202513 65.57465491679912 chr9 141213431 2695921133 19.09110991715795 56.6804812191331 chr10 135534747 3080881279 22.731302099232163 55.00177999850737 chr11 135006516 2868041930 21.24372967301815 52.195933017555454 chr12 133851895 2515162486 18.790637861346678 48.32861426721998 chr13 115169878 1353777635 11.754615516741278 36.523829404933785 chr14 107349540 1635230446 15.232766213995887 42.070290968702494 chr15 102531392 1911237562 18.64051121045933 50.28489340689863 chr16 90354753 1405054335 15.550419743829082 48.17343929973436 chr17 81195210 1347101052 16.590893132735292 41.65043829907406 chr18 78077248 2013645282 25.790423376602618 65.39139170547617 chr19 59128983 1310181646 22.158027747576853 56.80477754077915 chr20 63025520 1676339920 26.597795940438097 61.073871789993206 chr21 48129895 601193190 12.491055507185296 43.64426041066515 chr22 51304566 1066300962 20.783743926417777 57.3239300763703 chrMT 16571 5230513 315.64256834228473 581.9682488803965 chrX 155270560 1461019376 9.409506708805583 25.851284860184695 chrY 59373566 152120342 2.5620886911188725 19.666594458018672