BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6240038.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 = 1,926,768
number of mapped reads = 1,488,466 (77.25%)
number of supplementary alignments = 10,377 (0.54%)
number of secondary alignments = 0
number of mapped bases = 90,568,757 bp
number of sequenced bases = 90,518,871 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 276,103
duplication rate = 14.4%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.3063
>>>>>>> ACTG content
number of A's = 24,058,406 bp (26.58%)
number of C's = 15,827,803 bp (17.49%)
number of T's = 29,441,741 bp (32.53%)
number of G's = 21,135,455 bp (23.35%)
number of N's = 55,466 bp (0.06%)
GC percentage = 40.83%
>>>>>>> Mismatches and indels
general error rate = 0.0095
number of mismatches = 847,720
number of insertions = 5,928
mapped reads with insertion percentage = 0.4%
number of deletions = 29,400
mapped reads with deletion percentage = 1.95%
homopolymer indels = 45.6%
>>>>>>> Coverage
mean coverageData = 0.0293X
std coverageData = 0.3371X
There is a 1.59% of reference with a coverageData >= 1X
There is a 0.68% of reference with a coverageData >= 2X
There is a 0.32% of reference with a coverageData >= 3X
There is a 0.15% of reference with a coverageData >= 4X
There is a 0.07% of reference with a coverageData >= 5X
There is a 0.04% of reference with a coverageData >= 6X
There is a 0.02% 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% 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 4841155 0.019422840274488224 0.2730475596747483
chr2 243199373 9132072 0.037549734965805194 0.43480340012842755
chr3 198022430 8773744 0.04430681918204923 0.35097703656307466
chr4 191154276 4846005 0.025351276996806497 0.2676419826722625
chr5 180915260 4023351 0.022238870286563996 0.24547152001455777
chr6 171115067 6036258 0.035276016927252817 0.37397675790749174
chr7 159138663 4633105 0.029113635320663717 0.4917272209184547
chr8 146364022 8158069 0.05573821276925555 0.5847777502607845
chr9 141213431 4015841 0.02843809524038829 0.3036138139138814
chr10 135534747 4123296 0.0304224273942091 0.3170484106138101
chr11 135006516 3500108 0.02592547458968573 0.2984011971669226
chr12 133851895 2257957 0.016869070101697102 0.21436754499985938
chr13 115169878 1976500 0.017161605398244843 0.22077447265734085
chr14 107349540 2878584 0.02681505668305612 0.28307948674336736
chr15 102531392 4742529 0.04625440957633736 0.36605071637000264
chr16 90354753 1594724 0.017649586181703137 0.21741917134290864
chr17 81195210 1487319 0.018317817023935277 0.22511713777739237
chr18 78077248 2276959 0.02916290031124048 0.361685790996843
chr19 59128983 1796280 0.030379010577604556 0.30932667049982215
chr20 63025520 1591695 0.02525476981387857 0.2645343272776278
chr21 48129895 796192 0.01654256673528999 0.20736396165231402
chr22 51304566 696672 0.013579142254122177 0.1849835995318706
chrMT 16571 136455 8.234566411200289 7.780582346877737
chrX 155270560 6019653 0.0387687981546534 0.33357164235860837
chrY 59373566 234234 0.003945088964338103 0.1064370647415222