BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3124819.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 23,236,344
number of mapped reads = 22,421,096 (96.49%)
number of supplementary alignments = 30,145 (0.13%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 11,300,882
number of mapped paired reads (second in pair) = 11,120,214
number of mapped paired reads (both in pair) = 22,004,738
number of mapped paired reads (singletons) = 416,358
number of mapped bases = 1,463,796,834 bp
number of sequenced bases = 1,463,121,272 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 2,512,241
duplication rate = 7.02%
>>>>>>> Insert size
mean insert size = 42,382.4519
std insert size = 1,956,974.598
median insert size = 194
>>>>>>> Mapping quality
mean mapping quality = 51.9211
>>>>>>> ACTG content
number of A's = 415,384,309 bp (28.39%)
number of C's = 266,100,264 bp (18.19%)
number of T's = 440,831,345 bp (30.13%)
number of G's = 340,759,405 bp (23.29%)
number of N's = 45,949 bp (0%)
GC percentage = 41.48%
>>>>>>> Mismatches and indels
general error rate = 0.0084
number of mismatches = 11,927,349
number of insertions = 167,919
mapped reads with insertion percentage = 0.74%
number of deletions = 450,001
mapped reads with deletion percentage = 1.98%
homopolymer indels = 48.27%
>>>>>>> Coverage
mean coverageData = 0.4728X
std coverageData = 4.0991X
There is a 24.58% of reference with a coverageData >= 1X
There is a 10.33% of reference with a coverageData >= 2X
There is a 4.79% of reference with a coverageData >= 3X
There is a 2.4% of reference with a coverageData >= 4X
There is a 1.28% of reference with a coverageData >= 5X
There is a 0.73% of reference with a coverageData >= 6X
There is a 0.44% of reference with a coverageData >= 7X
There is a 0.28% of reference with a coverageData >= 8X
There is a 0.19% of reference with a coverageData >= 9X
There is a 0.13% of reference with a coverageData >= 10X
There is a 0.1% of reference with a coverageData >= 11X
There is a 0.07% of reference with a coverageData >= 12X
There is a 0.06% of reference with a coverageData >= 13X
There is a 0.05% of reference with a coverageData >= 14X
There is a 0.04% of reference with a coverageData >= 15X
There is a 0.03% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.03% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.02% of reference with a coverageData >= 22X
There is a 0.02% of reference with a coverageData >= 23X
There is a 0.02% 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 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 117210999 0.47025358865605393 4.256305174920655
chr2 243199373 148185831 0.609318310207979 4.07847086611925
chr3 198022430 130020092 0.65659275062931 1.585916825668066
chr4 191154276 83404668 0.4363212256889299 2.148467077681755
chr5 180915260 61255869 0.33858873485851887 0.9150821530478236
chr6 171115067 82759793 0.48364994650062 5.876874531760753
chr7 159138663 102860257 0.6463561717871162 5.9623488356364085
chr8 146364022 77458111 0.529215513085586 1.7266547477247314
chr9 141213431 42619612 0.30180990362028665 3.701062592806682
chr10 135534747 71303072 0.5260870262295174 12.101449962543974
chr11 135006516 76762610 0.5685844822482494 2.641543550785054
chr12 133851895 74086248 0.5534942034253606 1.214086584021794
chr13 115169878 44900145 0.38986014207638564 0.9562874069167249
chr14 107349540 62245156 0.5798362619905032 1.4320076149826542
chr15 102531392 42782930 0.4172666455167214 1.0537190101493752
chr16 90354753 41867000 0.46336245310747515 4.158482983632831
chr17 81195210 40044552 0.4931886006576004 3.031131203529482
chr18 78077248 25848728 0.33106607446000147 5.173313558675903
chr19 59128983 16405744 0.2774568945317392 3.0467261226575135
chr20 63025520 38644784 0.6131608910168452 1.394726619882999
chr21 48129895 10903824 0.22654992287018286 1.439279705230286
chr22 51304566 15267982 0.29759499378671284 0.9022779727075954
chrMT 16571 104779 6.3230342164021485 4.608768141915206
chrX 155270560 52885955 0.34060516687773906 1.5122126702340786
chrY 59373566 3968093 0.0668326541141221 3.9776477974768545