BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472458.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 = 13,276,624
number of mapped reads = 13,128,689 (98.89%)
number of supplementary alignments = 57,298 (0.43%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,589,179
number of mapped paired reads (second in pair) = 6,539,510
number of mapped paired reads (both in pair) = 13,057,202
number of mapped paired reads (singletons) = 71,487
number of mapped bases = 1,277,030,387 bp
number of sequenced bases = 1,276,883,308 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 8,386,142
duplication rate = 45.54%
>>>>>>> Insert size
mean insert size = 20,955.2818
std insert size = 1,458,256.4284
median insert size = 192
>>>>>>> Mapping quality
mean mapping quality = 54.8212
>>>>>>> ACTG content
number of A's = 341,219,981 bp (26.72%)
number of C's = 297,348,589 bp (23.29%)
number of T's = 343,587,150 bp (26.91%)
number of G's = 294,559,829 bp (23.07%)
number of N's = 167,759 bp (0.01%)
GC percentage = 46.36%
>>>>>>> Mismatches and indels
general error rate = 0.0045
number of mismatches = 5,618,921
number of insertions = 74,582
mapped reads with insertion percentage = 0.56%
number of deletions = 63,975
mapped reads with deletion percentage = 0.48%
homopolymer indels = 45.65%
>>>>>>> Coverage
mean coverageData = 0.4125X
std coverageData = 17.3068X
There is a 3.57% of reference with a coverageData >= 1X
There is a 1.68% of reference with a coverageData >= 2X
There is a 0.7% of reference with a coverageData >= 3X
There is a 0.53% of reference with a coverageData >= 4X
There is a 0.4% of reference with a coverageData >= 5X
There is a 0.36% of reference with a coverageData >= 6X
There is a 0.32% of reference with a coverageData >= 7X
There is a 0.3% of reference with a coverageData >= 8X
There is a 0.29% of reference with a coverageData >= 9X
There is a 0.28% of reference with a coverageData >= 10X
There is a 0.26% of reference with a coverageData >= 11X
There is a 0.25% of reference with a coverageData >= 12X
There is a 0.25% of reference with a coverageData >= 13X
There is a 0.24% of reference with a coverageData >= 14X
There is a 0.23% of reference with a coverageData >= 15X
There is a 0.22% of reference with a coverageData >= 16X
There is a 0.22% of reference with a coverageData >= 17X
There is a 0.21% of reference with a coverageData >= 18X
There is a 0.21% of reference with a coverageData >= 19X
There is a 0.2% of reference with a coverageData >= 20X
There is a 0.2% of reference with a coverageData >= 21X
There is a 0.19% of reference with a coverageData >= 22X
There is a 0.19% of reference with a coverageData >= 23X
There is a 0.18% of reference with a coverageData >= 24X
There is a 0.18% of reference with a coverageData >= 25X
There is a 0.18% of reference with a coverageData >= 26X
There is a 0.17% of reference with a coverageData >= 27X
There is a 0.17% of reference with a coverageData >= 28X
There is a 0.17% of reference with a coverageData >= 29X
There is a 0.16% of reference with a coverageData >= 30X
There is a 0.16% of reference with a coverageData >= 31X
There is a 0.16% of reference with a coverageData >= 32X
There is a 0.16% of reference with a coverageData >= 33X
There is a 0.15% of reference with a coverageData >= 34X
There is a 0.15% of reference with a coverageData >= 35X
There is a 0.15% of reference with a coverageData >= 36X
There is a 0.15% of reference with a coverageData >= 37X
There is a 0.14% of reference with a coverageData >= 38X
There is a 0.14% of reference with a coverageData >= 39X
There is a 0.14% of reference with a coverageData >= 40X
There is a 0.14% of reference with a coverageData >= 41X
There is a 0.14% of reference with a coverageData >= 42X
There is a 0.13% of reference with a coverageData >= 43X
There is a 0.13% of reference with a coverageData >= 44X
There is a 0.13% of reference with a coverageData >= 45X
There is a 0.13% of reference with a coverageData >= 46X
There is a 0.13% of reference with a coverageData >= 47X
There is a 0.13% of reference with a coverageData >= 48X
There is a 0.12% of reference with a coverageData >= 49X
There is a 0.12% of reference with a coverageData >= 50X
There is a 0.12% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 190157643 0.762917429200708 24.494002547700145
chr2 243199373 83442135 0.34310176860529984 13.049429538960906
chr3 198022430 108384240 0.5473331480681254 15.870469604921068
chr4 191154276 35231302 0.18430820768037645 7.71546659061898
chr5 180915260 57010249 0.31512128385410937 11.353904166025394
chr6 171115067 103740776 0.6062632462400287 29.550138532294763
chr7 159138663 69407868 0.4361471102720022 17.85730606481264
chr8 146364022 67446284 0.46081190635769764 16.512721543908064
chr9 141213431 62683182 0.44388966089210025 15.42517303602388
chr10 135534747 38451443 0.2837017359098328 11.17142093253705
chr11 135006516 56593319 0.41918953748869425 18.67360026380001
chr12 133851895 61453039 0.4591122075634417 14.274244842513731
chr13 115169878 19409355 0.16852805036400229 6.159179962829354
chr14 107349540 32231797 0.30025090931922016 14.126004302610385
chr15 102531392 23307383 0.22731948279800981 8.437405893221605
chr16 90354753 86178118 0.9537751489398681 35.135470457187765
chr17 81195210 41308429 0.50875450657742 15.097376818805282
chr18 78077248 33032164 0.4230702905922094 29.598287341049488
chr19 59128983 20032315 0.33879011583879265 11.260468919072697
chr20 63025520 22022234 0.3494177279298925 13.919327118504338
chr21 48129895 12951998 0.26910505414566144 16.140199705961845
chr22 51304566 14086306 0.2745624239370819 10.784898880715886
chrMT 16571 80319 4.846961559350673 9.537794743924133
chrX 155270560 36975067 0.23813314642518196 10.323895072952157
chrY 59373566 1413422 0.023805577047536608 2.442661101342879