BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672001.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 199,123,808 number of mapped reads = 198,020,641 (99.45%) number of supplementary alignments = 920,986 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 99,020,292 number of mapped paired reads (second in pair) = 99,000,349 number of mapped paired reads (both in pair) = 197,633,964 number of mapped paired reads (singletons) = 386,677 number of mapped bases = 29,340,854,475 bp number of sequenced bases = 29,328,676,210 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,745,678 duplication rate = 24.14% >>>>>>> Insert size mean insert size = 45,801.6093 std insert size = 2,042,049.0541 median insert size = 396 >>>>>>> Mapping quality mean mapping quality = 54.5198 >>>>>>> ACTG content number of A's = 8,530,037,466 bp (29.08%) number of C's = 6,143,396,735 bp (20.95%) number of T's = 8,490,650,698 bp (28.95%) number of G's = 6,164,462,788 bp (21.02%) number of N's = 128,523 bp (0%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 174,018,317 number of insertions = 4,213,181 mapped reads with insertion percentage = 2% number of deletions = 4,402,920 mapped reads with deletion percentage = 2.13% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 9.478X std coverageData = 96.6911X There is a 92.04% of reference with a coverageData >= 1X There is a 91.19% of reference with a coverageData >= 2X There is a 89.48% of reference with a coverageData >= 3X There is a 86.61% of reference with a coverageData >= 4X There is a 82.36% of reference with a coverageData >= 5X There is a 76.65% of reference with a coverageData >= 6X There is a 69.64% of reference with a coverageData >= 7X There is a 61.65% of reference with a coverageData >= 8X There is a 53.12% of reference with a coverageData >= 9X There is a 44.55% of reference with a coverageData >= 10X There is a 36.39% of reference with a coverageData >= 11X There is a 28.98% of reference with a coverageData >= 12X There is a 22.53% of reference with a coverageData >= 13X There is a 17.14% of reference with a coverageData >= 14X There is a 12.79% of reference with a coverageData >= 15X There is a 9.38% of reference with a coverageData >= 16X There is a 6.78% of reference with a coverageData >= 17X There is a 4.85% of reference with a coverageData >= 18X There is a 3.45% of reference with a coverageData >= 19X There is a 2.45% of reference with a coverageData >= 20X There is a 1.75% of reference with a coverageData >= 21X There is a 1.27% of reference with a coverageData >= 22X There is a 0.94% of reference with a coverageData >= 23X There is a 0.71% of reference with a coverageData >= 24X There is a 0.56% of reference with a coverageData >= 25X There is a 0.46% of reference with a coverageData >= 26X There is a 0.38% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.3% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2448180655 9.822164715890517 234.26237482384974 chr2 243199373 2527459018 10.392539202804606 65.6194357403738 chr3 198022430 1916007470 9.675709312323862 7.951960016667721 chr4 191154276 1863817875 9.750333154985244 63.99795485726183 chr5 180915260 1741129405 9.624005211058481 8.90745776829069 chr6 171115067 1679586963 9.81554104174824 52.00334383511636 chr7 159138663 1602837577 10.071955782360694 72.14231550363037 chr8 146364022 1459880619 9.9743133527719 67.10349135685713 chr9 141213431 1289698502 9.13297335010577 158.83925492443413 chr10 135534747 1523234979 11.238704558912852 167.60580029102712 chr11 135006516 1358617531 10.063347838707282 37.785896021554265 chr12 133851895 1310454826 9.790334503669149 8.493568052049483 chr13 115169878 904759443 7.855868728106146 6.780199741901207 chr14 107349540 894490202 8.332501489992412 8.26823103287028 chr15 102531392 845503297 8.246287117607844 6.089630854206703 chr16 90354753 984322947 10.893980829099272 63.8832487198525 chr17 81195210 900598558 11.091769551430435 59.98590383253051 chr18 78077248 821421834 10.52062995355574 144.7876645738007 chr19 59128983 664899420 11.244898631183966 98.5723546503982 chr20 63025520 653393052 10.367118779821253 26.337571642335682 chr21 48129895 416928850 8.662575515695599 40.61323295335604 chr22 51304566 414266614 8.07465390117519 35.955181814144346 chrMT 16571 76393079 4610.0464063725785 565.0960361240394 chrX 155270560 765195099 4.928140266899276 19.263653155225697 chrY 59373566 277776660 4.678456739485717 80.5621447340581