BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365357.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 = 546,294,286 number of mapped reads = 518,530,957 (94.92%) number of supplementary alignments = 2,143,033 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 259,885,336 number of mapped paired reads (second in pair) = 258,645,621 number of mapped paired reads (both in pair) = 515,839,778 number of mapped paired reads (singletons) = 2,691,179 number of mapped bases = 53,977,249,807 bp number of sequenced bases = 53,959,102,144 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 316,781,390 duplication rate = 31.41% >>>>>>> Insert size mean insert size = 51,286.2867 std insert size = 2,158,262.2119 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 53.7511 >>>>>>> ACTG content number of A's = 16,337,252,976 bp (30.28%) number of C's = 10,483,925,217 bp (19.43%) number of T's = 15,893,268,082 bp (29.45%) number of G's = 11,235,967,596 bp (20.82%) number of N's = 8,688,273 bp (0.02%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 315,240,791 number of insertions = 15,992,051 mapped reads with insertion percentage = 3.01% number of deletions = 8,584,201 mapped reads with deletion percentage = 1.61% homopolymer indels = 49.99% >>>>>>> Coverage mean coverageData = 17.4362X std coverageData = 183.9051X There is a 79.44% of reference with a coverageData >= 1X There is a 76.81% of reference with a coverageData >= 2X There is a 73.31% of reference with a coverageData >= 3X There is a 70.68% of reference with a coverageData >= 4X There is a 67.51% of reference with a coverageData >= 5X There is a 64.91% of reference with a coverageData >= 6X There is a 61.94% of reference with a coverageData >= 7X There is a 59.41% of reference with a coverageData >= 8X There is a 56.64% of reference with a coverageData >= 9X There is a 54.21% of reference with a coverageData >= 10X There is a 51.61% of reference with a coverageData >= 11X There is a 49.31% of reference with a coverageData >= 12X There is a 46.9% of reference with a coverageData >= 13X There is a 44.73% of reference with a coverageData >= 14X There is a 42.48% of reference with a coverageData >= 15X There is a 40.45% of reference with a coverageData >= 16X There is a 38.38% of reference with a coverageData >= 17X There is a 36.5% of reference with a coverageData >= 18X There is a 34.6% of reference with a coverageData >= 19X There is a 32.86% of reference with a coverageData >= 20X There is a 31.12% of reference with a coverageData >= 21X There is a 29.53% of reference with a coverageData >= 22X There is a 27.96% of reference with a coverageData >= 23X There is a 26.51% of reference with a coverageData >= 24X There is a 25.09% of reference with a coverageData >= 25X There is a 23.78% of reference with a coverageData >= 26X There is a 22.49% of reference with a coverageData >= 27X There is a 21.31% of reference with a coverageData >= 28X There is a 20.15% of reference with a coverageData >= 29X There is a 19.09% of reference with a coverageData >= 30X There is a 18.05% of reference with a coverageData >= 31X There is a 17.09% of reference with a coverageData >= 32X There is a 16.16% of reference with a coverageData >= 33X There is a 15.3% of reference with a coverageData >= 34X There is a 14.46% of reference with a coverageData >= 35X There is a 13.69% of reference with a coverageData >= 36X There is a 12.94% of reference with a coverageData >= 37X There is a 12.24% of reference with a coverageData >= 38X There is a 11.57% of reference with a coverageData >= 39X There is a 10.95% of reference with a coverageData >= 40X There is a 10.34% of reference with a coverageData >= 41X There is a 9.78% of reference with a coverageData >= 42X There is a 9.24% of reference with a coverageData >= 43X There is a 8.74% of reference with a coverageData >= 44X There is a 8.25% of reference with a coverageData >= 45X There is a 7.8% of reference with a coverageData >= 46X There is a 7.37% of reference with a coverageData >= 47X There is a 6.97% of reference with a coverageData >= 48X There is a 6.58% of reference with a coverageData >= 49X There is a 6.23% of reference with a coverageData >= 50X There is a 5.88% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3466495500 13.907670464740788 505.48474145003917 chr2 243199373 4715301339 19.38862457100167 107.23194343845448 chr3 198022430 3719651542 18.783990995363506 29.567843224058432 chr4 191154276 3830864561 20.0406950927951 106.07451171852159 chr5 180915260 3404380813 18.81754371079587 23.210459355062962 chr6 171115067 3242001173 18.946322085126496 78.99554477063367 chr7 159138663 3849773137 24.191312559915122 119.42071407450133 chr8 146364022 2772170111 18.94024278042865 58.53864911974157 chr9 141213431 2290027880 16.216785214998424 138.8755187645605 chr10 135534747 2789736996 20.58318665692422 339.30208289415674 chr11 135006516 2510410910 18.594738864307853 117.95527449401669 chr12 133851895 2415315184 18.044684268384845 36.55740502522953 chr13 115169878 1842646491 15.999378683026825 19.261831944298443 chr14 107349540 1653270104 15.400812187923675 21.961973765963084 chr15 102531392 1492476161 14.556284976605019 22.782644161507605 chr16 90354753 1526479942 16.894295997909484 68.9886900430943 chr17 81195210 1374669819 16.930429997040466 105.46382276848529 chr18 78077248 1535300241 19.663862140735286 176.91638077388154 chr19 59128983 966494186 16.34552358189553 257.8970879594109 chr20 63025520 1075235466 17.06031883592551 35.56641738922231 chr21 48129895 769041864 15.978465442320205 65.78817598101257 chr22 51304566 598664049 11.668825909179311 51.25892359381591 chrMT 16571 74911208 4520.620843642508 811.3363071704028 chrX 155270560 1505933968 9.698773341192304 46.92061733460266 chrY 59373566 555997162 9.3643888931987 208.03921581312434