BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3082324.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,007,558
number of mapped reads = 3,629,665 (90.57%)
number of supplementary alignments = 34,515 (0.86%)
number of secondary alignments = 0
number of mapped bases = 246,962,760 bp
number of sequenced bases = 246,875,278 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 167,615
duplication rate = 3.5%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.1061
>>>>>>> ACTG content
number of A's = 70,560,098 bp (28.58%)
number of C's = 45,874,810 bp (18.58%)
number of T's = 77,600,620 bp (31.43%)
number of G's = 52,834,631 bp (21.4%)
number of N's = 5,119 bp (0%)
GC percentage = 39.98%
>>>>>>> Mismatches and indels
general error rate = 0.0084
number of mismatches = 2,030,504
number of insertions = 19,357
mapped reads with insertion percentage = 0.53%
number of deletions = 54,715
mapped reads with deletion percentage = 1.49%
homopolymer indels = 48.01%
>>>>>>> Coverage
mean coverageData = 0.0798X
std coverageData = 0.6242X
There is a 6.6% of reference with a coverageData >= 1X
There is a 1.01% of reference with a coverageData >= 2X
There is a 0.18% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% 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 19333231 0.07756542761030874 1.0903999266737767
chr2 243199373 21129645 0.0868819879728884 0.713860775236071
chr3 198022430 17213609 0.08692757179073098 0.3400660437883233
chr4 191154276 16617888 0.08693442986334242 0.3584448959861969
chr5 180915260 15563001 0.0860237052418906 0.34269575064301816
chr6 171115067 14732524 0.08609717576769554 0.41087126285278325
chr7 159138663 13573199 0.08529164908215925 0.7579565738233344
chr8 146364022 12899489 0.08813292244729377 1.2632038965511774
chr9 141213431 10382531 0.07352367920300726 0.5551320090238427
chr10 135534747 11420926 0.08426566805042253 0.524505547993019
chr11 135006516 11214850 0.08306895350147396 0.5097035133529666
chr12 133851895 11097771 0.08291082468425269 0.3434007235902008
chr13 115169878 8300819 0.07207456623336876 0.3101310004648998
chr14 107349540 7583894 0.07064673029805252 0.34062989744544336
chr15 102531392 6886419 0.0671640057320201 0.3083016087715746
chr16 90354753 6458725 0.07148185109863561 0.3595591336044951
chr17 81195210 5912414 0.07281727579742697 0.3577498222418923
chr18 78077248 6800046 0.08709382277408138 1.0713482454592043
chr19 59128983 4174501 0.07059991206004676 0.8334857549470881
chr20 63025520 4710983 0.07474722937629075 0.33193695783369137
chr21 48129895 3301024 0.06858573034493426 0.3276708927041824
chr22 51304566 2352984 0.04586305242305334 0.24437239227332777
chrMT 16571 16745 1.0105002715587472 1.0916925053779876
chrX 155270560 14707428 0.09472129166018337 0.41852573959330536
chrY 59373566 578114 0.009736892003421186 0.20495108424630668