BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472589.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 = 10,102,094
number of mapped reads = 9,255,481 (91.62%)
number of supplementary alignments = 279,558 (2.77%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 4,670,702
number of mapped paired reads (second in pair) = 4,584,779
number of mapped paired reads (both in pair) = 9,043,652
number of mapped paired reads (singletons) = 211,829
number of mapped bases = 751,735,641 bp
number of sequenced bases = 751,411,787 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,514,126
duplication rate = 14.29%
>>>>>>> Insert size
mean insert size = 217,136.9355
std insert size = 4,453,904.1853
median insert size = 126
>>>>>>> Mapping quality
mean mapping quality = 50.5696
>>>>>>> ACTG content
number of A's = 194,560,947 bp (25.89%)
number of C's = 151,163,320 bp (20.12%)
number of T's = 222,559,116 bp (29.62%)
number of G's = 182,650,981 bp (24.31%)
number of N's = 477,423 bp (0.06%)
GC percentage = 44.42%
>>>>>>> Mismatches and indels
general error rate = 0.0117
number of mismatches = 8,649,920
number of insertions = 69,968
mapped reads with insertion percentage = 0.74%
number of deletions = 172,449
mapped reads with deletion percentage = 1.83%
homopolymer indels = 42.77%
>>>>>>> Coverage
mean coverageData = 0.2428X
std coverageData = 2.1847X
There is a 12.93% of reference with a coverageData >= 1X
There is a 6.09% of reference with a coverageData >= 2X
There is a 2.23% of reference with a coverageData >= 3X
There is a 1.1% of reference with a coverageData >= 4X
There is a 0.52% of reference with a coverageData >= 5X
There is a 0.29% of reference with a coverageData >= 6X
There is a 0.16% of reference with a coverageData >= 7X
There is a 0.1% of reference with a coverageData >= 8X
There is a 0.06% of reference with a coverageData >= 9X
There is a 0.04% of reference with a coverageData >= 10X
There is a 0.03% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.02% of reference with a coverageData >= 13X
There is a 0.02% 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% 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 47051613 0.18877229998957556 2.6285318584435746
chr2 243199373 70646616 0.2904884791787683 3.147658274558454
chr3 198022430 36935721 0.18652291561112547 0.6601890390616391
chr4 191154276 35040975 0.18331253547265666 1.1393368357503504
chr5 180915260 33283998 0.1839756248312055 0.6819250333653271
chr6 171115067 45850578 0.26795172864584743 1.2180625981793831
chr7 159138663 66591341 0.41844853880668836 3.8160682200042686
chr8 146364022 34138461 0.23324352893226724 1.7778772083388312
chr9 141213431 23717116 0.16795226793972592 2.2408951435740643
chr10 135534747 39250216 0.2895952282996478 2.1125306501101226
chr11 135006516 37796181 0.2799581984620653 2.0616650445206823
chr12 133851895 35689865 0.2666369796258768 0.8269545049341754
chr13 115169878 32691167 0.2838517116428655 0.8535714724733232
chr14 107349540 18366748 0.17109293621565588 5.25802011892482
chr15 102531392 20504534 0.19998298667397396 0.7046263074868262
chr16 90354753 26560947 0.2939629196927803 1.2438767576255372
chr17 81195210 23292378 0.28686886824974034 1.6171341137825965
chr18 78077248 15694011 0.20100620093577068 3.5476905458143806
chr19 59128983 12640156 0.21377259270635518 1.90251620257785
chr20 63025520 29257980 0.4642243332542119 1.5170728218601957
chr21 48129895 11101898 0.2306653276513485 0.9850081227005701
chr22 51304566 7237612 0.14107149839256022 0.5867205244870883
chrMT 16571 857069 51.72101864703397 29.164640937979616
chrX 155270560 45623729 0.2938337377027558 1.1903692570655175
chrY 59373566 1914731 0.032248879914000786 0.9680121106975897