BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6068116.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 = 1,976,536
number of mapped reads = 1,496,045 (75.69%)
number of supplementary alignments = 15,696 (0.79%)
number of secondary alignments = 0
number of mapped bases = 99,930,368 bp
number of sequenced bases = 99,891,994 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 239,468
duplication rate = 11.31%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.7801
>>>>>>> ACTG content
number of A's = 27,839,844 bp (27.87%)
number of C's = 18,045,962 bp (18.07%)
number of T's = 32,122,999 bp (32.16%)
number of G's = 21,779,825 bp (21.8%)
number of N's = 103,364 bp (0.1%)
GC percentage = 39.87%
>>>>>>> Mismatches and indels
general error rate = 0.009
number of mismatches = 880,261
number of insertions = 8,030
mapped reads with insertion percentage = 0.53%
number of deletions = 23,294
mapped reads with deletion percentage = 1.54%
homopolymer indels = 48%
>>>>>>> Coverage
mean coverageData = 0.0323X
std coverageData = 0.4617X
There is a 1.24% of reference with a coverageData >= 1X
There is a 0.64% of reference with a coverageData >= 2X
There is a 0.41% of reference with a coverageData >= 3X
There is a 0.27% of reference with a coverageData >= 4X
There is a 0.19% of reference with a coverageData >= 5X
There is a 0.13% of reference with a coverageData >= 6X
There is a 0.09% of reference with a coverageData >= 7X
There is a 0.06% of reference with a coverageData >= 8X
There is a 0.04% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% 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% 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 8290587 0.033262051531658975 0.6121337349512443
chr2 243199373 8256608 0.03394995594828281 0.4947025301146642
chr3 198022430 6287636 0.03175214040146866 0.40304751960089874
chr4 191154276 6745178 0.03528656612421267 0.4338385164175717
chr5 180915260 6347564 0.0350858407411293 0.42835792930249633
chr6 171115067 5822164 0.034024847151536926 0.4263461227014579
chr7 159138663 5599419 0.035185786372982156 0.5088179560009706
chr8 146364022 4850104 0.03313726921223851 0.6135350305800844
chr9 141213431 4333754 0.030689389594959985 0.4326933909503271
chr10 135534747 4600426 0.033942779263829666 0.4858948005631772
chr11 135006516 4787706 0.03546277721884179 0.4524871549239637
chr12 133851895 4933989 0.03686155507921647 0.4288102096235014
chr13 115169878 3134904 0.027219825656149433 0.3735453821327541
chr14 107349540 2883404 0.026859956735725183 0.373325729296711
chr15 102531392 2478807 0.02417607867842075 0.34892938361429365
chr16 90354753 2781908 0.030788728955963168 0.3929096997179116
chr17 81195210 2556671 0.03148795353814591 0.38551098167084125
chr18 78077248 2834660 0.03630583905826189 0.6253202454975293
chr19 59128983 1760016 0.029765707284361714 0.46723657831170834
chr20 63025520 1976830 0.031365548431809845 0.3881875112226579
chr21 48129895 1397908 0.02904448472202152 0.3751241109463657
chr22 51304566 1099788 0.02143645460328034 0.3030129299407979
chrMT 16571 18683 1.1274515720234144 2.08850223887264
chrX 155270560 5830429 0.03755012540690263 0.4530176176014352
chrY 59373566 321225 0.005410235928898055 0.15965373586200513