BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6063569.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,951,902
number of mapped reads = 1,398,502 (71.65%)
number of supplementary alignments = 15,509 (0.79%)
number of secondary alignments = 0
number of mapped bases = 90,618,879 bp
number of sequenced bases = 90,578,328 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 92,966
duplication rate = 5.24%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9687
>>>>>>> ACTG content
number of A's = 26,057,255 bp (28.77%)
number of C's = 16,855,593 bp (18.61%)
number of T's = 29,645,257 bp (32.73%)
number of G's = 18,018,568 bp (19.89%)
number of N's = 1,655 bp (0%)
GC percentage = 38.5%
>>>>>>> Mismatches and indels
general error rate = 0.0087
number of mismatches = 771,617
number of insertions = 8,071
mapped reads with insertion percentage = 0.57%
number of deletions = 24,511
mapped reads with deletion percentage = 1.73%
homopolymer indels = 47.31%
>>>>>>> Coverage
mean coverageData = 0.0293X
std coverageData = 0.3442X
There is a 2.05% of reference with a coverageData >= 1X
There is a 0.56% of reference with a coverageData >= 2X
There is a 0.17% of reference with a coverageData >= 3X
There is a 0.06% of reference with a coverageData >= 4X
There is a 0.02% 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 10263822 0.04117872187768792 0.6399500031807405
chr2 243199373 14519160 0.05970064733678405 0.4606243567900963
chr3 198022430 5273994 0.026633316235943574 0.25085792470038215
chr4 191154276 3332999 0.017436172863849513 0.19347489695601416
chr5 180915260 2998736 0.016575362410003444 0.22500000766958214
chr6 171115067 3231287 0.01888370823593226 0.21838879623091165
chr7 159138663 8832810 0.055503859549203324 0.36948205978203813
chr8 146364022 3120228 0.02131827178129882 0.2950673253075553
chr9 141213431 3669346 0.025984398042138073 0.2560308140165419
chr10 135534747 3064102 0.022607501528740817 0.6284326266925747
chr11 135006516 3591608 0.026603219654968358 0.24886402150609685
chr12 133851895 5892354 0.04402144624101138 0.2851600931894881
chr13 115169878 1550131 0.013459517600600393 0.1609624254136707
chr14 107349540 1426275 0.013286270253230708 0.17177163760324868
chr15 102531392 1351625 0.013182548033679286 0.16864201109761753
chr16 90354753 1297038 0.014354950425242156 0.1816732626400299
chr17 81195210 1953394 0.02405799553939204 0.21774417245878466
chr18 78077248 1525576 0.019539315729980647 0.4015907194993206
chr19 59128983 1484968 0.025114046016993054 0.33359995454084024
chr20 63025520 1736184 0.027547317340658198 0.22743174118537846
chr21 48129895 1880862 0.0390788718737076 0.27275981645086983
chr22 51304566 1161611 0.022641474055155247 0.19786774527350356
chrMT 16571 48966 2.9549212479633096 3.0622835156505834
chrX 155270560 7102591 0.04574332056250715 0.30034081283841646
chrY 59373566 309212 0.0052079068318045775 0.10391569474079432