BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR630495.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 103,479,816
number of mapped reads = 103,146,198 (99.68%)
number of supplementary alignments = 524,245 (0.51%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 51,667,361
number of mapped paired reads (second in pair) = 51,478,837
number of mapped paired reads (both in pair) = 102,929,674
number of mapped paired reads (singletons) = 216,524
number of mapped bases = 10,302,200,797 bp
number of sequenced bases = 10,300,059,919 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 15,991,532
duplication rate = 13.57%
>>>>>>> Insert size
mean insert size = 32,942.8777
std insert size = 1,721,931.6356
median insert size = 238
>>>>>>> Mapping quality
mean mapping quality = 53.9554
>>>>>>> ACTG content
number of A's = 3,206,903,891 bp (31.13%)
number of C's = 1,937,359,659 bp (18.81%)
number of T's = 3,196,536,724 bp (31.03%)
number of G's = 1,958,381,317 bp (19.01%)
number of N's = 878,328 bp (0.01%)
GC percentage = 37.82%
>>>>>>> Mismatches and indels
general error rate = 0.0071
number of mismatches = 71,119,185
number of insertions = 880,684
mapped reads with insertion percentage = 0.84%
number of deletions = 944,420
mapped reads with deletion percentage = 0.89%
homopolymer indels = 44.63%
>>>>>>> Coverage
mean coverageData = 3.3279X
std coverageData = 11.1293X
There is a 41.2% of reference with a coverageData >= 1X
There is a 29.24% of reference with a coverageData >= 2X
There is a 22.91% of reference with a coverageData >= 3X
There is a 18.84% of reference with a coverageData >= 4X
There is a 15.96% of reference with a coverageData >= 5X
There is a 13.79% of reference with a coverageData >= 6X
There is a 12.09% of reference with a coverageData >= 7X
There is a 10.73% of reference with a coverageData >= 8X
There is a 9.61% of reference with a coverageData >= 9X
There is a 8.68% of reference with a coverageData >= 10X
There is a 7.88% of reference with a coverageData >= 11X
There is a 7.2% of reference with a coverageData >= 12X
There is a 6.61% of reference with a coverageData >= 13X
There is a 6.09% of reference with a coverageData >= 14X
There is a 5.63% of reference with a coverageData >= 15X
There is a 5.23% of reference with a coverageData >= 16X
There is a 4.87% of reference with a coverageData >= 17X
There is a 4.54% of reference with a coverageData >= 18X
There is a 4.25% of reference with a coverageData >= 19X
There is a 3.98% of reference with a coverageData >= 20X
There is a 3.74% of reference with a coverageData >= 21X
There is a 3.52% of reference with a coverageData >= 22X
There is a 3.32% of reference with a coverageData >= 23X
There is a 3.13% of reference with a coverageData >= 24X
There is a 2.96% of reference with a coverageData >= 25X
There is a 2.81% of reference with a coverageData >= 26X
There is a 2.66% of reference with a coverageData >= 27X
There is a 2.53% of reference with a coverageData >= 28X
There is a 2.4% of reference with a coverageData >= 29X
There is a 2.28% of reference with a coverageData >= 30X
There is a 2.18% of reference with a coverageData >= 31X
There is a 2.07% of reference with a coverageData >= 32X
There is a 1.98% of reference with a coverageData >= 33X
There is a 1.89% of reference with a coverageData >= 34X
There is a 1.81% of reference with a coverageData >= 35X
There is a 1.73% of reference with a coverageData >= 36X
There is a 1.65% of reference with a coverageData >= 37X
There is a 1.58% of reference with a coverageData >= 38X
There is a 1.52% of reference with a coverageData >= 39X
There is a 1.45% of reference with a coverageData >= 40X
There is a 1.39% of reference with a coverageData >= 41X
There is a 1.34% of reference with a coverageData >= 42X
There is a 1.29% of reference with a coverageData >= 43X
There is a 1.24% of reference with a coverageData >= 44X
There is a 1.19% of reference with a coverageData >= 45X
There is a 1.14% of reference with a coverageData >= 46X
There is a 1.1% of reference with a coverageData >= 47X
There is a 1.06% of reference with a coverageData >= 48X
There is a 1.02% of reference with a coverageData >= 49X
There is a 0.98% of reference with a coverageData >= 50X
There is a 0.95% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 794464757 3.187413350516788 11.372926153333573
chr2 243199373 918053465 3.7749006244354093 11.583388461459235
chr3 198022430 745121085 3.7628115410966325 10.759566955423201
chr4 191154276 851008915 4.451948095579091 12.757347230119525
chr5 180915260 703839420 3.890436992435022 11.500802032689096
chr6 171115067 670329398 3.91741890268494 12.536964900258763
chr7 159138663 590448277 3.7102754658684045 13.744868185820076
chr8 146364022 552211122 3.77286107920702 10.8785369889523
chr9 141213431 352724786 2.4978132993596054 8.098874986507587
chr10 135534747 432100083 3.188112956746066 9.985116623024549
chr11 135006516 539367115 3.9951191318795307 12.717393643434358
chr12 133851895 465635418 3.4787360911102527 10.12567473004806
chr13 115169878 393155691 3.4137024179186852 10.683539414782521
chr14 107349540 321024262 2.990457732748552 10.276289332676724
chr15 102531392 238121903 2.322429241963281 8.18723161298025
chr16 90354753 180705642 1.9999572352325505 10.844397746347607
chr17 81195210 153157893 1.8862922209327373 7.363023960607823
chr18 78077248 244007815 3.1252102405043782 9.149996210750476
chr19 59128983 54501417 0.921737771136703 3.564500843689984
chr20 63025520 155496363 2.4671968275708 9.472457974534583
chr21 48129895 112425864 2.335884256551983 8.672761621442458
chr22 51304566 42210750 0.8227484080071937 3.674051452928464
chrMT 16571 5845 0.3527246394303301 1.6546524924314643
chrX 155270560 786390516 5.064646614271243 16.3033006811489
chrY 59373566 5692995 0.09588433681076187 1.3998484433006955