BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1818889.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 = 2,045,805
number of mapped reads = 2,017,204 (98.6%)
number of supplementary alignments = 30,662 (1.5%)
number of secondary alignments = 0
number of mapped bases = 186,905,625 bp
number of sequenced bases = 186,792,763 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 316,013
duplication rate = 12.36%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.2265
>>>>>>> ACTG content
number of A's = 53,350,855 bp (28.56%)
number of C's = 38,661,605 bp (20.7%)
number of T's = 52,480,943 bp (28.1%)
number of G's = 42,296,851 bp (22.64%)
number of N's = 2,509 bp (0%)
GC percentage = 43.34%
>>>>>>> Mismatches and indels
general error rate = 0.0065
number of mismatches = 1,144,606
number of insertions = 28,803
mapped reads with insertion percentage = 1.39%
number of deletions = 55,721
mapped reads with deletion percentage = 2.7%
homopolymer indels = 39.01%
>>>>>>> Coverage
mean coverageData = 0.0604X
std coverageData = 0.7894X
There is a 4.52% of reference with a coverageData >= 1X
There is a 0.91% of reference with a coverageData >= 2X
There is a 0.24% of reference with a coverageData >= 3X
There is a 0.08% of reference with a coverageData >= 4X
There is a 0.03% of reference with a coverageData >= 5X
There is a 0.02% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% 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 17819355 0.07149171756727539 1.2912223646553975
chr2 243199373 14052072 0.0577800502799816 0.9099971868929222
chr3 198022430 11347969 0.057306482907012096 0.3048850556941101
chr4 191154276 9324521 0.04878008065066774 0.47159096348591617
chr5 180915260 8153901 0.04507027765374795 0.2753911682578531
chr6 171115067 9179502 0.05364520004541739 0.3415119022124803
chr7 159138663 16665597 0.10472374648516433 1.7474645292446889
chr8 146364022 16040363 0.10959225348426131 0.6373182561941734
chr9 141213431 6844699 0.04847059484023159 0.676502320275167
chr10 135534747 9074547 0.06695365727874934 1.378463898048252
chr11 135006516 8154222 0.0603987291991151 0.4335550517926764
chr12 133851895 7194563 0.05375017664113011 0.29054582146054625
chr13 115169878 5590748 0.04854349155427602 0.2718622197097785
chr14 107349540 5407185 0.05036989445879321 0.3076622414073813
chr15 102531392 5089748 0.04964087486493893 0.2754740144096999
chr16 90354753 4886578 0.054082135557384566 0.6226202120385742
chr17 81195210 4861155 0.05986997262523245 0.5163207940835625
chr18 78077248 3593778 0.04602849219275761 0.802961705779432
chr19 59128983 3453363 0.05840389644448984 1.09756132454674
chr20 63025520 7917917 0.12563033196711426 0.4991920788299267
chr21 48129895 1861655 0.03867980597090436 0.3910123380893819
chr22 51304566 1765949 0.034420893454200546 0.25311082518512573
chrMT 16571 278128 16.784020276386457 10.097722538845629
chrX 155270560 7546981 0.04860535699748877 0.38368587248672203
chrY 59373566 801129 0.013493024825222726 0.9316379327621854