BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238265.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 = 2,577,063
number of mapped reads = 2,359,047 (91.54%)
number of supplementary alignments = 27,043 (1.05%)
number of secondary alignments = 0
number of mapped bases = 155,154,284 bp
number of sequenced bases = 155,071,865 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 111,020
duplication rate = 3.44%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3832
>>>>>>> ACTG content
number of A's = 43,741,041 bp (28.21%)
number of C's = 29,387,499 bp (18.95%)
number of T's = 47,956,612 bp (30.93%)
number of G's = 33,944,521 bp (21.89%)
number of N's = 42,192 bp (0.03%)
GC percentage = 40.84%
>>>>>>> Mismatches and indels
general error rate = 0.0091
number of mismatches = 1,388,692
number of insertions = 13,134
mapped reads with insertion percentage = 0.55%
number of deletions = 49,558
mapped reads with deletion percentage = 2.08%
homopolymer indels = 45.36%
>>>>>>> Coverage
mean coverageData = 0.0501X
std coverageData = 0.4666X
There is a 4.1% of reference with a coverageData >= 1X
There is a 0.65% of reference with a coverageData >= 2X
There is a 0.12% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0% 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 14981953 0.06010798665171631 0.8256442653530935
chr2 243199373 18245152 0.07502137762501551 0.6071696060013182
chr3 198022430 10385591 0.05244653850576422 0.2675109820564965
chr4 191154276 6963371 0.03642801587132689 0.25951670250371617
chr5 180915260 13367053 0.07388571312337058 0.3245796740366474
chr6 171115067 6891420 0.0402736013889414 0.30175455172812526
chr7 159138663 6876203 0.043208877530911516 0.36546760768641345
chr8 146364022 6727077 0.045961274554207045 0.6410331237054689
chr9 141213431 5936978 0.0420425872946887 0.501786012029162
chr10 135534747 8010220 0.05910085920623735 0.4793972219740895
chr11 135006516 7810592 0.05785344464410888 0.4251236778634673
chr12 133851895 5131671 0.03833842621353997 0.2518478692561381
chr13 115169878 3101275 0.02692783090384102 0.19225949493823505
chr14 107349540 3594506 0.0334841304396833 0.3103325996292355
chr15 102531392 4735271 0.04618362150003776 0.2530997082540568
chr16 90354753 4819722 0.053342207686628285 0.337620816168151
chr17 81195210 5074811 0.06250135937821948 0.35785453764800856
chr18 78077248 5120325 0.0655802443241852 0.9840871788159107
chr19 59128983 3372641 0.05703871145559869 0.6632219025804977
chr20 63025520 4060173 0.06442109482000308 0.3073282491440973
chr21 48129895 1675460 0.03481121244914413 0.27134439426294404
chr22 51304566 1899994 0.03703362386887748 0.22192214035213675
chrMT 16571 2855 0.17228893850703036 0.5082034318642662
chrX 155270560 6014627 0.03873642885038864 0.292284150217379
chrY 59373566 355343 0.005984868754556531 0.19761684691924822