BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975265.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,211,316 number of mapped reads = 5,112,677 (98.11%) number of supplementary alignments = 70,957 (1.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,565,379 number of mapped paired reads (second in pair) = 2,547,298 number of mapped paired reads (both in pair) = 5,077,658 number of mapped paired reads (singletons) = 35,019 number of mapped bases = 705,049,376 bp number of sequenced bases = 704,566,915 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 628,250 duplication rate = 9.58% >>>>>>> Insert size mean insert size = 51,742.9975 std insert size = 2,146,121.7514 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 53.5226 >>>>>>> ACTG content number of A's = 204,609,555 bp (29.04%) number of C's = 141,872,376 bp (20.14%) number of T's = 206,073,251 bp (29.25%) number of G's = 151,954,790 bp (21.57%) number of N's = 56,943 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 7,721,867 number of insertions = 119,865 mapped reads with insertion percentage = 2.21% number of deletions = 244,753 mapped reads with deletion percentage = 4.6% homopolymer indels = 47.29% >>>>>>> Coverage mean coverageData = 0.2278X std coverageData = 3.1212X There is a 12.51% of reference with a coverageData >= 1X There is a 6.19% of reference with a coverageData >= 2X There is a 1.68% of reference with a coverageData >= 3X There is a 0.73% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 60754465 0.24374850002881238 3.4478343617044267 chr2 243199373 67868383 0.27906479429944914 2.787213445549345 chr3 198022430 25217647 0.12734742725861914 0.5736485050268099 chr4 191154276 35813061 0.18735160808016663 2.372425167210558 chr5 180915260 47189239 0.2608361450548726 0.7649801899027976 chr6 171115067 37879563 0.22136895168909937 2.7055654516728125 chr7 159138663 18530311 0.11644128868922318 1.5486028032256143 chr8 146364022 35706569 0.24395728207031644 1.0202778326960333 chr9 141213431 27924327 0.19774554588932833 4.030686365460303 chr10 135534747 32480861 0.23964969661986382 10.542777954141402 chr11 135006516 31528440 0.23353272815365445 3.1542730390571294 chr12 133851895 38799502 0.28986890323816483 0.7721677947990608 chr13 115169878 19632498 0.17046556218458442 0.5736686492343513 chr14 107349540 23315629 0.21719356226398362 0.6985941734003895 chr15 102531392 17966607 0.17523030410042614 0.5892547795499371 chr16 90354753 13207854 0.14617774451776766 1.9818849566563712 chr17 81195210 11446303 0.14097263865688628 1.3362331401928833 chr18 78077248 18139399 0.23232631098882994 4.33805046824548 chr19 59128983 12674948 0.21436100127073046 1.810825281230576 chr20 63025520 22287100 0.3536202477980348 1.1762623357392012 chr21 48129895 7935867 0.16488436137249002 1.2456313420894536 chr22 51304566 5486986 0.10694927231233181 0.48212907789925885 chrMT 16571 141877 8.561764528392976 5.762219888595208 chrX 155270560 90776087 0.5846316713226255 2.130928186369706 chrY 59373566 2345853 0.03951005738816496 2.206710607795816