BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472567.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 207,827,342 number of mapped reads = 205,317,284 (98.79%) number of supplementary alignments = 94,329 (0.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 102,857,499 number of mapped paired reads (second in pair) = 102,459,785 number of mapped paired reads (both in pair) = 204,734,168 number of mapped paired reads (singletons) = 583,116 number of mapped bases = 18,820,752,580 bp number of sequenced bases = 18,817,827,361 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,093,335 duplication rate = 47.95% >>>>>>> Insert size mean insert size = 4,220.1555 std insert size = 606,292.1469 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 51.6809 >>>>>>> ACTG content number of A's = 4,368,720,268 bp (23.22%) number of C's = 5,062,027,967 bp (26.9%) number of T's = 4,465,798,782 bp (23.73%) number of G's = 4,919,003,464 bp (26.14%) number of N's = 2,276,880 bp (0.01%) GC percentage = 53.04% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 94,481,149 number of insertions = 984,807 mapped reads with insertion percentage = 0.46% number of deletions = 1,228,313 mapped reads with deletion percentage = 0.58% homopolymer indels = 38.23% >>>>>>> Coverage mean coverageData = 6.0797X std coverageData = 76.9967X There is a 51% of reference with a coverageData >= 1X There is a 38.53% of reference with a coverageData >= 2X There is a 25.2% of reference with a coverageData >= 3X There is a 19.19% of reference with a coverageData >= 4X There is a 13.53% of reference with a coverageData >= 5X There is a 10.71% of reference with a coverageData >= 6X There is a 8.36% of reference with a coverageData >= 7X There is a 7.08% of reference with a coverageData >= 8X There is a 6.08% of reference with a coverageData >= 9X There is a 5.48% of reference with a coverageData >= 10X There is a 5.02% of reference with a coverageData >= 11X There is a 4.7% of reference with a coverageData >= 12X There is a 4.45% of reference with a coverageData >= 13X There is a 4.26% of reference with a coverageData >= 14X There is a 4.1% of reference with a coverageData >= 15X There is a 3.97% of reference with a coverageData >= 16X There is a 3.86% of reference with a coverageData >= 17X There is a 3.75% of reference with a coverageData >= 18X There is a 3.66% of reference with a coverageData >= 19X There is a 3.58% of reference with a coverageData >= 20X There is a 3.5% of reference with a coverageData >= 21X There is a 3.43% of reference with a coverageData >= 22X There is a 3.36% of reference with a coverageData >= 23X There is a 3.29% of reference with a coverageData >= 24X There is a 3.23% of reference with a coverageData >= 25X There is a 3.17% of reference with a coverageData >= 26X There is a 3.11% of reference with a coverageData >= 27X There is a 3.06% of reference with a coverageData >= 28X There is a 3.01% of reference with a coverageData >= 29X There is a 2.96% of reference with a coverageData >= 30X There is a 2.91% of reference with a coverageData >= 31X There is a 2.87% of reference with a coverageData >= 32X There is a 2.82% of reference with a coverageData >= 33X There is a 2.78% of reference with a coverageData >= 34X There is a 2.74% of reference with a coverageData >= 35X There is a 2.7% of reference with a coverageData >= 36X There is a 2.66% of reference with a coverageData >= 37X There is a 2.62% of reference with a coverageData >= 38X There is a 2.58% of reference with a coverageData >= 39X There is a 2.55% of reference with a coverageData >= 40X There is a 2.51% of reference with a coverageData >= 41X There is a 2.48% of reference with a coverageData >= 42X There is a 2.44% of reference with a coverageData >= 43X There is a 2.41% of reference with a coverageData >= 44X There is a 2.38% of reference with a coverageData >= 45X There is a 2.35% of reference with a coverageData >= 46X There is a 2.32% of reference with a coverageData >= 47X There is a 2.29% of reference with a coverageData >= 48X There is a 2.26% of reference with a coverageData >= 49X There is a 2.23% of reference with a coverageData >= 50X There is a 2.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1805903031 7.245330116950842 50.426351021371296 chr2 243199373 1241852332 5.106313871952294 42.373810597042954 chr3 198022430 982055074 4.959312306186728 34.171392154940655 chr4 191154276 766633141 4.010546648718441 39.19652401703889 chr5 180915260 934224799 5.163880586966517 51.29953020079197 chr6 171115067 836483080 4.888424465859573 30.878048409232854 chr7 159138663 1271674924 7.990986602671156 258.02894630206646 chr8 146364022 1068945194 7.303333014448045 134.67692615154755 chr9 141213431 836241945 5.921830091360078 39.32157321804305 chr10 135534747 755628312 5.575163039187287 36.149760020440745 chr11 135006516 1005652356 7.448917176708715 42.748641989973564 chr12 133851895 785953230 5.871812498433436 32.07568519650459 chr13 115169878 348215614 3.0234955532383214 19.79478041397311 chr14 107349540 510780430 4.758105437619947 31.191945120334722 chr15 102531392 768650996 7.496738130698548 47.969757225830655 chr16 90354753 850347752 9.411212180503664 49.63433959200835 chr17 81195210 961476843 11.841546354766495 65.71372988794361 chr18 78077248 326960793 4.187657754023298 39.685123551760405 chr19 59128983 938946839 15.879637892638877 62.92797492519073 chr20 63025520 443552402 7.03766350519599 45.32118534192921 chr21 48129895 248927012 5.171983275675129 46.867377531086035 chr22 51304566 502728614 9.79890589075444 60.151772128108696 chrMT 16571 48070232 2900.8648844366667 973.1936143519974 chrX 155270560 420053114 2.705297862002945 17.690332994940217 chrY 59373566 160794521 2.7081836553324083 46.969116162223166