BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514717.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 78,878,010 number of mapped reads = 73,327,108 (92.96%) number of supplementary alignments = 3,657,343 (4.64%) number of secondary alignments = 0 number of mapped bases = 6,974,319,199 bp number of sequenced bases = 6,969,237,095 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,012,553 duplication rate = 33.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1438 >>>>>>> ACTG content number of A's = 1,899,644,382 bp (27.26%) number of C's = 1,570,292,552 bp (22.53%) number of T's = 1,917,288,915 bp (27.51%) number of G's = 1,581,728,502 bp (22.7%) number of N's = 282,744 bp (0%) GC percentage = 45.23% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 66,006,115 number of insertions = 3,668,290 mapped reads with insertion percentage = 4.73% number of deletions = 2,192,106 mapped reads with deletion percentage = 2.82% homopolymer indels = 40.69% >>>>>>> Coverage mean coverageData = 2.2529X std coverageData = 104.6053X There is a 12.39% of reference with a coverageData >= 1X There is a 7.1% of reference with a coverageData >= 2X There is a 4.91% of reference with a coverageData >= 3X There is a 3.8% of reference with a coverageData >= 4X There is a 3.12% of reference with a coverageData >= 5X There is a 2.67% of reference with a coverageData >= 6X There is a 2.34% of reference with a coverageData >= 7X There is a 2.1% of reference with a coverageData >= 8X There is a 1.91% of reference with a coverageData >= 9X There is a 1.75% of reference with a coverageData >= 10X There is a 1.62% of reference with a coverageData >= 11X There is a 1.52% of reference with a coverageData >= 12X There is a 1.43% of reference with a coverageData >= 13X There is a 1.35% of reference with a coverageData >= 14X There is a 1.28% of reference with a coverageData >= 15X There is a 1.22% of reference with a coverageData >= 16X There is a 1.16% of reference with a coverageData >= 17X There is a 1.12% of reference with a coverageData >= 18X There is a 1.07% of reference with a coverageData >= 19X There is a 1.03% of reference with a coverageData >= 20X There is a 0.99% of reference with a coverageData >= 21X There is a 0.96% of reference with a coverageData >= 22X There is a 0.93% of reference with a coverageData >= 23X There is a 0.9% of reference with a coverageData >= 24X There is a 0.88% of reference with a coverageData >= 25X There is a 0.85% of reference with a coverageData >= 26X There is a 0.83% of reference with a coverageData >= 27X There is a 0.81% of reference with a coverageData >= 28X There is a 0.79% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.75% of reference with a coverageData >= 31X There is a 0.73% of reference with a coverageData >= 32X There is a 0.72% of reference with a coverageData >= 33X There is a 0.7% of reference with a coverageData >= 34X There is a 0.69% of reference with a coverageData >= 35X There is a 0.67% of reference with a coverageData >= 36X There is a 0.66% of reference with a coverageData >= 37X There is a 0.65% of reference with a coverageData >= 38X There is a 0.63% of reference with a coverageData >= 39X There is a 0.62% of reference with a coverageData >= 40X There is a 0.61% of reference with a coverageData >= 41X There is a 0.6% of reference with a coverageData >= 42X There is a 0.59% of reference with a coverageData >= 43X There is a 0.58% of reference with a coverageData >= 44X There is a 0.57% of reference with a coverageData >= 45X There is a 0.56% of reference with a coverageData >= 46X There is a 0.55% of reference with a coverageData >= 47X There is a 0.55% of reference with a coverageData >= 48X There is a 0.54% of reference with a coverageData >= 49X There is a 0.53% of reference with a coverageData >= 50X There is a 0.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 507510100 2.036143773539485 59.70039294765442 chr2 243199373 525445223 2.160553362117426 100.94119169329802 chr3 198022430 506371315 2.5571412036505157 56.293066012644864 chr4 191154276 376625658 1.9702706415000626 57.17119231195148 chr5 180915260 385221488 2.1292923991044206 57.418064120014705 chr6 171115067 451128468 2.63640412214548 135.37365673015591 chr7 159138663 487464849 3.0631453086922065 129.4753870001175 chr8 146364022 283669094 1.9381067158703797 62.665860769513145 chr9 141213431 304369054 2.155383180230215 77.21153733770045 chr10 135534747 371868247 2.7437115221825734 55.585045254850364 chr11 135006516 362997682 2.688741941907456 70.63882199594224 chr12 133851895 349428780 2.61056281646218 64.68318668813305 chr13 115169878 174733699 1.517182287889547 66.67658476891778 chr14 107349540 242693970 2.2607825799719308 71.8857466734794 chr15 102531392 218355057 2.1296410078973667 69.57089028237105 chr16 90354753 176557085 1.954043137055557 74.68945165405516 chr17 81195210 223502739 2.752659165485255 78.11569328214664 chr18 78077248 184972860 2.3691006629741866 55.71916965930706 chr19 59128983 139175401 2.3537594245448124 78.05558197221832 chr20 63025520 205204052 3.2558882814453574 482.02216729187364 chr21 48129895 65074334 1.3520564297927515 61.74076114579108 chr22 51304566 136740182 2.665263399752763 171.63023778346033 chrMT 16571 526892 31.796029207651923 21.876508909976067 chrX 155270560 184960260 1.191212680626643 35.71701494495495 chrY 59373566 109722710 1.8480060638432936 37.54295659505817