BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365365.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 = 576,647,552 number of mapped reads = 492,000,162 (85.32%) number of supplementary alignments = 19,466,705 (3.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 244,637,639 number of mapped paired reads (second in pair) = 247,362,523 number of mapped paired reads (both in pair) = 477,682,998 number of mapped paired reads (singletons) = 14,317,164 number of mapped bases = 61,542,552,477 bp number of sequenced bases = 61,509,219,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 348,903,867 duplication rate = 46.32% >>>>>>> Insert size mean insert size = 125,830.624 std insert size = 3,457,232.4174 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 53.0945 >>>>>>> ACTG content number of A's = 17,226,597,478 bp (28.01%) number of C's = 12,832,781,921 bp (20.86%) number of T's = 17,564,677,315 bp (28.56%) number of G's = 13,883,316,082 bp (22.57%) number of N's = 1,846,524 bp (0%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 635,465,000 number of insertions = 6,051,219 mapped reads with insertion percentage = 1.17% number of deletions = 15,844,016 mapped reads with deletion percentage = 3.12% homopolymer indels = 43.08% >>>>>>> Coverage mean coverageData = 19.8801X std coverageData = 194.6026X There is a 38.22% of reference with a coverageData >= 1X There is a 32.1% of reference with a coverageData >= 2X There is a 26.69% of reference with a coverageData >= 3X There is a 24.95% of reference with a coverageData >= 4X There is a 23.49% of reference with a coverageData >= 5X There is a 22.71% of reference with a coverageData >= 6X There is a 21.95% of reference with a coverageData >= 7X There is a 21.44% of reference with a coverageData >= 8X There is a 20.9% of reference with a coverageData >= 9X There is a 20.5% of reference with a coverageData >= 10X There is a 20.06% of reference with a coverageData >= 11X There is a 19.72% of reference with a coverageData >= 12X There is a 19.34% of reference with a coverageData >= 13X There is a 19.03% of reference with a coverageData >= 14X There is a 18.69% of reference with a coverageData >= 15X There is a 18.4% of reference with a coverageData >= 16X There is a 18.1% of reference with a coverageData >= 17X There is a 17.83% of reference with a coverageData >= 18X There is a 17.55% of reference with a coverageData >= 19X There is a 17.3% of reference with a coverageData >= 20X There is a 17.04% of reference with a coverageData >= 21X There is a 16.8% of reference with a coverageData >= 22X There is a 16.56% of reference with a coverageData >= 23X There is a 16.33% of reference with a coverageData >= 24X There is a 16.1% of reference with a coverageData >= 25X There is a 15.88% of reference with a coverageData >= 26X There is a 15.66% of reference with a coverageData >= 27X There is a 15.46% of reference with a coverageData >= 28X There is a 15.24% of reference with a coverageData >= 29X There is a 15.05% of reference with a coverageData >= 30X There is a 14.84% of reference with a coverageData >= 31X There is a 14.65% of reference with a coverageData >= 32X There is a 14.46% of reference with a coverageData >= 33X There is a 14.27% of reference with a coverageData >= 34X There is a 14.08% of reference with a coverageData >= 35X There is a 13.91% of reference with a coverageData >= 36X There is a 13.73% of reference with a coverageData >= 37X There is a 13.55% of reference with a coverageData >= 38X There is a 13.38% of reference with a coverageData >= 39X There is a 13.21% of reference with a coverageData >= 40X There is a 13.04% of reference with a coverageData >= 41X There is a 12.88% of reference with a coverageData >= 42X There is a 12.71% of reference with a coverageData >= 43X There is a 12.56% of reference with a coverageData >= 44X There is a 12.4% of reference with a coverageData >= 45X There is a 12.24% of reference with a coverageData >= 46X There is a 12.09% of reference with a coverageData >= 47X There is a 11.94% of reference with a coverageData >= 48X There is a 11.79% of reference with a coverageData >= 49X There is a 11.65% of reference with a coverageData >= 50X There is a 11.5% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5054381077 20.278308863270595 385.4979408993056 chr2 243199373 5335236742 21.93770763545513 243.2351973822118 chr3 198022430 4167743888 21.046827311431336 63.359475966665876 chr4 191154276 3980662555 20.82434480827413 109.27530064245978 chr5 180915260 3754453989 20.752555583205087 75.74483974466683 chr6 171115067 3615158146 21.12705917357938 100.39141068237768 chr7 159138663 3399180867 21.35986819871674 235.61665970451537 chr8 146364022 3147758996 21.5063712583684 110.79843523053941 chr9 141213431 2685339518 19.01617642871378 272.74754140115925 chr10 135534747 3088591087 22.78818646409544 236.5017101274473 chr11 135006516 2905580191 21.521777445171608 278.4166376864102 chr12 133851895 2734209179 20.42712341876071 63.270325092884356 chr13 115169878 1965851341 17.06914494604223 56.30375758610113 chr14 107349540 1950808263 18.172488331109758 162.64171212538986 chr15 102531392 1776767808 17.32901283540557 58.57394045043579 chr16 90354753 1856097188 20.54233038520951 82.81883980501662 chr17 81195210 1729775345 21.30390875274539 158.80328813594406 chr18 78077248 1727902924 22.1306842679701 311.88533023465203 chr19 59128983 1255612825 21.23515002786366 217.6969304773419 chr20 63025520 1389643910 22.048908283501667 83.18717137305987 chr21 48129895 864583755 17.963549577658544 103.68431789702144 chr22 51304566 760055959 14.814587048645924 80.21582602973417 chrMT 16571 39685969 2394.9048940920884 1396.0079640351514 chrX 155270560 1862262925 11.99366399528668 84.9728390830424 chrY 59373566 495208030 8.340547205805358 134.19345470741473