BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438252.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 = 787,729,130 number of mapped reads = 783,272,873 (99.43%) number of supplementary alignments = 21,233,256 (2.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 391,985,990 number of mapped paired reads (second in pair) = 391,286,883 number of mapped paired reads (both in pair) = 780,481,608 number of mapped paired reads (singletons) = 2,791,265 number of mapped bases = 110,725,784,106 bp number of sequenced bases = 110,690,454,720 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 335,540,317 duplication rate = 37.78% >>>>>>> Insert size mean insert size = 112,445.8013 std insert size = 3,250,794.3081 median insert size = 462 >>>>>>> Mapping quality mean mapping quality = 54.2468 >>>>>>> ACTG content number of A's = 34,072,881,211 bp (30.78%) number of C's = 20,930,199,869 bp (18.91%) number of T's = 32,091,985,284 bp (28.99%) number of G's = 23,595,183,800 bp (21.32%) number of N's = 204,556 bp (0%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 619,500,423 number of insertions = 14,627,632 mapped reads with insertion percentage = 1.82% number of deletions = 12,997,456 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.03% >>>>>>> Coverage mean coverageData = 35.7677X std coverageData = 126.6405X There is a 90.87% of reference with a coverageData >= 1X There is a 90.13% of reference with a coverageData >= 2X There is a 89.37% of reference with a coverageData >= 3X There is a 88.56% of reference with a coverageData >= 4X There is a 87.69% of reference with a coverageData >= 5X There is a 86.75% of reference with a coverageData >= 6X There is a 85.74% of reference with a coverageData >= 7X There is a 84.65% of reference with a coverageData >= 8X There is a 83.49% of reference with a coverageData >= 9X There is a 82.26% of reference with a coverageData >= 10X There is a 80.96% of reference with a coverageData >= 11X There is a 79.6% of reference with a coverageData >= 12X There is a 78.17% of reference with a coverageData >= 13X There is a 76.69% of reference with a coverageData >= 14X There is a 75.16% of reference with a coverageData >= 15X There is a 73.58% of reference with a coverageData >= 16X There is a 71.97% of reference with a coverageData >= 17X There is a 70.32% of reference with a coverageData >= 18X There is a 68.65% of reference with a coverageData >= 19X There is a 66.95% of reference with a coverageData >= 20X There is a 65.25% of reference with a coverageData >= 21X There is a 63.53% of reference with a coverageData >= 22X There is a 61.81% of reference with a coverageData >= 23X There is a 60.09% of reference with a coverageData >= 24X There is a 58.38% of reference with a coverageData >= 25X There is a 56.68% of reference with a coverageData >= 26X There is a 55% of reference with a coverageData >= 27X There is a 53.33% of reference with a coverageData >= 28X There is a 51.68% of reference with a coverageData >= 29X There is a 50.05% of reference with a coverageData >= 30X There is a 48.45% of reference with a coverageData >= 31X There is a 46.88% of reference with a coverageData >= 32X There is a 45.34% of reference with a coverageData >= 33X There is a 43.83% of reference with a coverageData >= 34X There is a 42.35% of reference with a coverageData >= 35X There is a 40.91% of reference with a coverageData >= 36X There is a 39.5% of reference with a coverageData >= 37X There is a 38.13% of reference with a coverageData >= 38X There is a 36.79% of reference with a coverageData >= 39X There is a 35.49% of reference with a coverageData >= 40X There is a 34.23% of reference with a coverageData >= 41X There is a 33% of reference with a coverageData >= 42X There is a 31.81% of reference with a coverageData >= 43X There is a 30.66% of reference with a coverageData >= 44X There is a 29.54% of reference with a coverageData >= 45X There is a 28.46% of reference with a coverageData >= 46X There is a 27.41% of reference with a coverageData >= 47X There is a 26.39% of reference with a coverageData >= 48X There is a 25.41% of reference with a coverageData >= 49X There is a 24.47% of reference with a coverageData >= 50X There is a 23.55% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8606200123 34.52829962257145 46.00533890723288 chr2 243199373 9597691432 39.4642934873027 271.14563571932734 chr3 198022430 7799175257 39.38531234567721 28.841306700437663 chr4 191154276 7710419573 40.3361082699505 39.29088693725454 chr5 180915260 7130624538 39.414168478656805 29.293694435521164 chr6 171115067 6719772958 39.27049251600971 35.15673201878623 chr7 159138663 5935811489 37.29961894300947 31.62244975752101 chr8 146364022 5623103782 38.41862026721294 32.29111223204044 chr9 141213431 4660739910 33.004933574625774 55.5189630457516 chr10 135534747 5049517877 37.25626076536668 88.87909256484934 chr11 135006516 4999682254 37.032895908520445 31.98429412564133 chr12 133851895 4994556489 37.31405139239904 30.916422648035372 chr13 115169878 3805505282 33.04253983841157 29.678888520693796 chr14 107349540 3364862423 31.344917015946226 30.55820743167375 chr15 102531392 3013277142 29.388825053696724 29.2375071063783 chr16 90354753 2841614503 31.44952986590534 89.17028404904522 chr17 81195210 2461396174 30.314549023273663 48.871457885794854 chr18 78077248 3003531693 38.4687187360907 66.78390595951711 chr19 59128983 1471944737 24.893794249767495 33.68016779492482 chr20 63025520 2100088915 33.321246932988416 32.770360760288156 chr21 48129895 1436807106 29.852695627114915 46.753006318213814 chr22 51304566 1011305761 19.71180812639561 27.55006445187514 chrMT 16571 617994056 37293.709251101325 13721.899140968293 chrX 155270560 6627658095 42.68457649022455 32.95240819054902 chrY 59373566 142502537 2.400100694642461 38.7692254428802