BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6013182.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 = 1,413,033
number of mapped reads = 1,279,047 (90.52%)
number of supplementary alignments = 8,099 (0.57%)
number of secondary alignments = 0
number of mapped bases = 85,671,283 bp
number of sequenced bases = 85,627,784 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 33,745
duplication rate = 1.88%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6103
>>>>>>> ACTG content
number of A's = 24,312,816 bp (28.39%)
number of C's = 15,850,682 bp (18.51%)
number of T's = 26,799,611 bp (31.3%)
number of G's = 18,643,734 bp (21.77%)
number of N's = 20,941 bp (0.02%)
GC percentage = 40.28%
>>>>>>> Mismatches and indels
general error rate = 0.0084
number of mismatches = 703,935
number of insertions = 6,413
mapped reads with insertion percentage = 0.5%
number of deletions = 25,100
mapped reads with deletion percentage = 1.94%
homopolymer indels = 46.05%
>>>>>>> Coverage
mean coverageData = 0.0277X
std coverageData = 0.2785X
There is a 2.49% of reference with a coverageData >= 1X
There is a 0.19% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% 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 6268524 0.025149481974610605 0.45863862246348164
chr2 243199373 8690070 0.035732287845988815 0.31395059627004174
chr3 198022430 5460706 0.02757619932247069 0.1792745805771685
chr4 191154276 5499207 0.028768422632617436 0.18634850475832265
chr5 180915260 4757053 0.02629437118792522 0.17610416247516084
chr6 171115067 4605901 0.026916980957614915 0.20984410722965044
chr7 159138663 5399091 0.03392695966033094 0.49056809405583146
chr8 146364022 4714513 0.03221087351644381 0.34691968162769177
chr9 141213431 3077340 0.021792119759486618 0.23003131018783848
chr10 135534747 4048427 0.029870030303004145 0.2784829730909285
chr11 135006516 3584767 0.026552548026644876 0.2211071411524694
chr12 133851895 4240408 0.031679850330098056 0.1928594577244412
chr13 115169878 2255948 0.019588003731322873 0.15154246415312045
chr14 107349540 2894925 0.0269672790400406 0.1896328923483512
chr15 102531392 2346119 0.02288195794708415 0.16272583907609395
chr16 90354753 2710884 0.030002671801891815 0.20597137908164564
chr17 81195210 2129484 0.026226719531854157 0.18897098278956825
chr18 78077248 2108416 0.027004230476975827 0.4217493773031338
chr19 59128983 1660929 0.028089930110923776 0.3376041967721123
chr20 63025520 1882790 0.029873454435600057 0.18949487946379673
chr21 48129895 1449468 0.03011575238217328 0.19545303339062803
chr22 51304566 802579 0.015643422458733985 0.1349798009365714
chrMT 16571 206396 12.455253153098788 8.293734178934777
chrX 155270560 4685679 0.03017751079148552 0.20270246396294028
chrY 59373566 191659 0.0032280190143876486 0.07786998816204191