BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432726.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 = 375,478,790 number of mapped reads = 375,346,486 (99.96%) number of supplementary alignments = 5,089,653 (1.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 187,676,278 number of mapped paired reads (second in pair) = 187,670,208 number of mapped paired reads (both in pair) = 375,294,720 number of mapped paired reads (singletons) = 51,766 number of mapped bases = 51,358,385,834 bp number of sequenced bases = 51,306,782,471 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 182,205,469 duplication rate = 31.46% >>>>>>> Insert size mean insert size = 81,711.5026 std insert size = 2,903,575.4047 median insert size = 306 >>>>>>> Mapping quality mean mapping quality = 57.3889 >>>>>>> ACTG content number of A's = 14,304,964,644 bp (27.88%) number of C's = 10,770,920,174 bp (20.99%) number of T's = 14,140,945,834 bp (27.56%) number of G's = 12,077,224,401 bp (23.54%) number of N's = 12,727,418 bp (0.02%) GC percentage = 44.53% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 411,864,371 number of insertions = 11,331,468 mapped reads with insertion percentage = 2.96% number of deletions = 35,369,327 mapped reads with deletion percentage = 8.99% homopolymer indels = 52.33% >>>>>>> Coverage mean coverageData = 16.5903X std coverageData = 43.9139X There is a 61.46% of reference with a coverageData >= 1X There is a 53.48% of reference with a coverageData >= 2X There is a 48.07% of reference with a coverageData >= 3X There is a 43.95% of reference with a coverageData >= 4X There is a 40.62% of reference with a coverageData >= 5X There is a 37.83% of reference with a coverageData >= 6X There is a 35.44% of reference with a coverageData >= 7X There is a 33.36% of reference with a coverageData >= 8X There is a 31.52% of reference with a coverageData >= 9X There is a 29.89% of reference with a coverageData >= 10X There is a 28.42% of reference with a coverageData >= 11X There is a 27.08% of reference with a coverageData >= 12X There is a 25.87% of reference with a coverageData >= 13X There is a 24.75% of reference with a coverageData >= 14X There is a 23.73% of reference with a coverageData >= 15X There is a 22.78% of reference with a coverageData >= 16X There is a 21.9% of reference with a coverageData >= 17X There is a 21.08% of reference with a coverageData >= 18X There is a 20.31% of reference with a coverageData >= 19X There is a 19.6% of reference with a coverageData >= 20X There is a 18.93% of reference with a coverageData >= 21X There is a 18.29% of reference with a coverageData >= 22X There is a 17.7% of reference with a coverageData >= 23X There is a 17.13% of reference with a coverageData >= 24X There is a 16.6% of reference with a coverageData >= 25X There is a 16.1% of reference with a coverageData >= 26X There is a 15.62% of reference with a coverageData >= 27X There is a 15.16% of reference with a coverageData >= 28X There is a 14.73% of reference with a coverageData >= 29X There is a 14.31% of reference with a coverageData >= 30X There is a 13.92% of reference with a coverageData >= 31X There is a 13.54% of reference with a coverageData >= 32X There is a 13.18% of reference with a coverageData >= 33X There is a 12.84% of reference with a coverageData >= 34X There is a 12.51% of reference with a coverageData >= 35X There is a 12.19% of reference with a coverageData >= 36X There is a 11.89% of reference with a coverageData >= 37X There is a 11.6% of reference with a coverageData >= 38X There is a 11.32% of reference with a coverageData >= 39X There is a 11.05% of reference with a coverageData >= 40X There is a 10.79% of reference with a coverageData >= 41X There is a 10.54% of reference with a coverageData >= 42X There is a 10.3% of reference with a coverageData >= 43X There is a 10.07% of reference with a coverageData >= 44X There is a 9.84% of reference with a coverageData >= 45X There is a 9.63% of reference with a coverageData >= 46X There is a 9.42% of reference with a coverageData >= 47X There is a 9.22% of reference with a coverageData >= 48X There is a 9.02% of reference with a coverageData >= 49X There is a 8.83% of reference with a coverageData >= 50X There is a 8.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4665642656 18.718680167300366 47.852590208566156 chr2 243199373 4377190189 17.998361323900287 48.370868109304205 chr3 198022430 3546714872 17.910672402111217 43.819889809549615 chr4 191154276 2469621014 12.919517500095054 34.65302965644146 chr5 180915260 3029537339 16.74561526208458 42.42319826413127 chr6 171115067 3092802915 18.07440437141634 45.579671801660545 chr7 159138663 2466033031 15.496127619219724 40.057578230255025 chr8 146364022 2344848006 16.020658451159534 40.39918559584021 chr9 141213431 2600623506 18.416261736463298 49.64302764859545 chr10 135534747 2759120147 20.35728997966846 48.814520036139015 chr11 135006516 2406907105 17.82808101647479 44.17284104894257 chr12 133851895 2490784240 18.60850935281865 46.46116961100972 chr13 115169878 1380471852 11.98639675558222 34.63393946319157 chr14 107349540 1282377954 11.945816945279878 32.83428210422691 chr15 102531392 1423198085 13.880608243375843 38.77929219771524 chr16 90354753 1981522086 21.930468738041927 57.35954520036722 chr17 81195210 1869979832 23.030666858303587 54.88243160271285 chr18 78077248 1166918660 14.945694038806286 38.92631345896267 chr19 59128983 1380075167 23.340079551173744 58.14366728841449 chr20 63025520 1473436736 23.378414585076012 53.159213154322345 chr21 48129895 647882884 13.461132296257867 39.901354512570514 chr22 51304566 903323731 17.607082593779275 48.65102044884691 chrMT 16571 5280537 318.6613360690363 469.5937267197298 chrX 155270560 1512623651 9.741857381077264 26.955125457469798 chrY 59373566 81469639 1.372153375460049 14.410522360329963