BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1818958.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,167,197
number of mapped reads = 3,034,870 (95.82%)
number of supplementary alignments = 38,684 (1.22%)
number of secondary alignments = 0
number of mapped bases = 281,512,227 bp
number of sequenced bases = 281,350,471 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,634,510
duplication rate = 42.65%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.3508
>>>>>>> ACTG content
number of A's = 80,848,921 bp (28.74%)
number of C's = 55,963,025 bp (19.89%)
number of T's = 81,043,835 bp (28.81%)
number of G's = 63,483,046 bp (22.56%)
number of N's = 11,644 bp (0%)
GC percentage = 42.45%
>>>>>>> Mismatches and indels
general error rate = 0.0066
number of mismatches = 1,761,641
number of insertions = 38,591
mapped reads with insertion percentage = 1.23%
number of deletions = 87,652
mapped reads with deletion percentage = 2.83%
homopolymer indels = 42.98%
>>>>>>> Coverage
mean coverageData = 0.0909X
std coverageData = 1.0228X
There is a 3.21% of reference with a coverageData >= 1X
There is a 1.83% of reference with a coverageData >= 2X
There is a 1.18% of reference with a coverageData >= 3X
There is a 0.79% of reference with a coverageData >= 4X
There is a 0.55% of reference with a coverageData >= 5X
There is a 0.38% of reference with a coverageData >= 6X
There is a 0.27% of reference with a coverageData >= 7X
There is a 0.19% of reference with a coverageData >= 8X
There is a 0.14% of reference with a coverageData >= 9X
There is a 0.1% of reference with a coverageData >= 10X
There is a 0.07% of reference with a coverageData >= 11X
There is a 0.05% of reference with a coverageData >= 12X
There is a 0.04% of reference with a coverageData >= 13X
There is a 0.03% of reference with a coverageData >= 14X
There is a 0.02% of reference with a coverageData >= 15X
There is a 0.02% 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% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% 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 31963967 0.12824027026195453 1.5837479566442156
chr2 243199373 24998587 0.10279050760546163 1.7136487953421453
chr3 198022430 19333218 0.09763145518414253 0.7023733641329065
chr4 191154276 18302498 0.0957472591405698 0.7644905022286433
chr5 180915260 13655566 0.07548045421928476 0.6472869423443253
chr6 171115067 15364553 0.08979076635022444 0.719743867008836
chr7 159138663 13813993 0.08680475718210602 0.7867947749331611
chr8 146364022 17896399 0.12227321137704182 0.8897351104124888
chr9 141213431 10094896 0.07148679788114488 0.9980830962671027
chr10 135534747 14346247 0.10584921813444637 1.231079313564152
chr11 135006516 10437996 0.07731475716327647 0.7272767510391891
chr12 133851895 13451724 0.10049707551768318 0.7362092077055159
chr13 115169878 4765238 0.04137573194268731 0.44808258812027196
chr14 107349540 6527073 0.060802058397269335 0.6140628029535075
chr15 102531392 8313124 0.08107881730504546 0.6498972064868819
chr16 90354753 8485191 0.09390973599363389 1.2735460342610103
chr17 81195210 5912093 0.07281332236224279 0.6732556034018087
chr18 78077248 7158661 0.09168690218179822 1.3470760767500958
chr19 59128983 4476717 0.07571104343194944 1.4169619659539274
chr20 63025520 6123177 0.09715393066173829 0.758010319738487
chr21 48129895 4023324 0.0835930350564862 0.7145704261940266
chr22 51304566 3592084 0.07001489886884532 0.6605103318378637
chrMT 16571 238476 14.391165288757469 12.793944408245359
chrX 155270560 17374240 0.11189655012514929 0.8554047654779304
chrY 59373566 863185 0.014538203752154621 1.053206239341328