BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438290.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 834,873,472 number of mapped reads = 832,320,660 (99.69%) number of supplementary alignments = 13,456,402 (1.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 416,313,920 number of mapped paired reads (second in pair) = 416,006,740 number of mapped paired reads (both in pair) = 830,621,128 number of mapped paired reads (singletons) = 1,699,532 number of mapped bases = 119,312,667,966 bp number of sequenced bases = 119,280,821,186 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 361,374,430 duplication rate = 40.13% >>>>>>> Insert size mean insert size = 41,891.0794 std insert size = 2,034,358.1602 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 55.1501 >>>>>>> ACTG content number of A's = 35,687,246,138 bp (29.92%) number of C's = 24,217,937,611 bp (20.3%) number of T's = 34,101,442,398 bp (28.59%) number of G's = 25,273,457,408 bp (21.19%) number of N's = 737,631 bp (0%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 607,624,659 number of insertions = 14,829,598 mapped reads with insertion percentage = 1.75% number of deletions = 13,075,029 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.51% >>>>>>> Coverage mean coverageData = 38.5415X std coverageData = 84.1842X There is a 91.19% of reference with a coverageData >= 1X There is a 90.64% of reference with a coverageData >= 2X There is a 90.01% of reference with a coverageData >= 3X There is a 89.31% of reference with a coverageData >= 4X There is a 88.51% of reference with a coverageData >= 5X There is a 87.61% of reference with a coverageData >= 6X There is a 86.62% of reference with a coverageData >= 7X There is a 85.53% of reference with a coverageData >= 8X There is a 84.35% of reference with a coverageData >= 9X There is a 83.09% of reference with a coverageData >= 10X There is a 81.75% of reference with a coverageData >= 11X There is a 80.35% of reference with a coverageData >= 12X There is a 78.89% of reference with a coverageData >= 13X There is a 77.37% of reference with a coverageData >= 14X There is a 75.81% of reference with a coverageData >= 15X There is a 74.22% of reference with a coverageData >= 16X There is a 72.59% of reference with a coverageData >= 17X There is a 70.94% of reference with a coverageData >= 18X There is a 69.28% of reference with a coverageData >= 19X There is a 67.6% of reference with a coverageData >= 20X There is a 65.93% of reference with a coverageData >= 21X There is a 64.25% of reference with a coverageData >= 22X There is a 62.58% of reference with a coverageData >= 23X There is a 60.92% of reference with a coverageData >= 24X There is a 59.27% of reference with a coverageData >= 25X There is a 57.64% of reference with a coverageData >= 26X There is a 56.03% of reference with a coverageData >= 27X There is a 54.44% of reference with a coverageData >= 28X There is a 52.88% of reference with a coverageData >= 29X There is a 51.34% of reference with a coverageData >= 30X There is a 49.84% of reference with a coverageData >= 31X There is a 48.36% of reference with a coverageData >= 32X There is a 46.91% of reference with a coverageData >= 33X There is a 45.5% of reference with a coverageData >= 34X There is a 44.12% of reference with a coverageData >= 35X There is a 42.77% of reference with a coverageData >= 36X There is a 41.46% of reference with a coverageData >= 37X There is a 40.18% of reference with a coverageData >= 38X There is a 38.93% of reference with a coverageData >= 39X There is a 37.72% of reference with a coverageData >= 40X There is a 36.54% of reference with a coverageData >= 41X There is a 35.39% of reference with a coverageData >= 42X There is a 34.27% of reference with a coverageData >= 43X There is a 33.19% of reference with a coverageData >= 44X There is a 32.14% of reference with a coverageData >= 45X There is a 31.12% of reference with a coverageData >= 46X There is a 30.13% of reference with a coverageData >= 47X There is a 29.18% of reference with a coverageData >= 48X There is a 28.25% of reference with a coverageData >= 49X There is a 27.35% of reference with a coverageData >= 50X There is a 26.48% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10850264424 43.531544196232915 41.09594189022963 chr2 243199373 10531025964 43.30202760843466 166.00690182663305 chr3 198022430 8616665000 43.51358075951295 109.43011456538405 chr4 191154276 6868539283 35.93191544927826 31.245594564657623 chr5 180915260 7119714534 39.35386398029663 35.04177595199356 chr6 171115067 6978463534 40.782285606678926 34.567538759150565 chr7 159138663 6288594277 39.51644533421774 34.27392910094378 chr8 146364022 5805018761 39.66151436450687 32.976626355264635 chr9 141213431 5085451882 36.01252264736773 38.57386453403666 chr10 135534747 5852235772 43.1788593075693 45.05856998974609 chr11 135006516 5835939354 43.22709397226427 36.79065838787548 chr12 133851895 5830014641 43.55571238644025 35.56112259247199 chr13 115169878 3721334292 32.31169778611731 31.437900919291042 chr14 107349540 4028170177 37.523869939265694 37.372336858555315 chr15 102531392 3819511256 37.252115488688574 37.810567109327316 chr16 90354753 3446537558 38.14450755014515 52.71013495952753 chr17 81195210 3565142261 43.90828302556272 44.96077133101928 chr18 78077248 2818841037 36.103232493542805 31.321825949058084 chr19 59128983 2102028814 35.54988953555991 153.93218456003314 chr20 63025520 2860628464 45.38841510550012 39.04314142025935 chr21 48129895 1545318115 32.10724052067847 70.91297783616866 chr22 51304566 1614018306 31.4595450627143 40.02181275184471 chrMT 16571 333346529 20116.259067044837 7610.300145274585 chrX 155270560 3349971100 21.575056469172264 26.105946457932554 chrY 59373566 445892631 7.50995200456715 23.67294877063856