BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524683.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,925,097
number of mapped reads = 1,773,504 (92.13%)
number of supplementary alignments = 7,655 (0.4%)
number of secondary alignments = 0
number of mapped bases = 104,309,738 bp
number of sequenced bases = 104,278,501 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 77,541
duplication rate = 3.25%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6927
>>>>>>> ACTG content
number of A's = 27,073,433 bp (25.96%)
number of C's = 19,401,299 bp (18.61%)
number of T's = 33,539,418 bp (32.16%)
number of G's = 24,250,238 bp (23.26%)
number of N's = 14,113 bp (0.01%)
GC percentage = 41.86%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 521,446
number of insertions = 7,897
mapped reads with insertion percentage = 0.44%
number of deletions = 19,763
mapped reads with deletion percentage = 1.11%
homopolymer indels = 42.91%
>>>>>>> Coverage
mean coverageData = 0.0337X
std coverageData = 0.3108X
There is a 2.99% of reference with a coverageData >= 1X
There is a 0.27% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% 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 8356706 0.033527322686189014 0.5217888205911821
chr2 243199373 8878476 0.036506985566940583 0.45577793869392047
chr3 198022430 6927041 0.03498109279842693 0.20609001960150666
chr4 191154276 6712132 0.03511369005420522 0.23920656959327535
chr5 180915260 6287572 0.034754237978598376 0.2070432437605463
chr6 171115067 6013433 0.03514262715392561 0.24075033472954996
chr7 159138663 5781594 0.036330542754402805 0.3684695371593872
chr8 146364022 5280404 0.03607719935436046 0.3549247576389079
chr9 141213431 4355896 0.030846187711422435 0.2542536294128933
chr10 135534747 5058547 0.03732287927611655 0.31323638321062597
chr11 135006516 4659525 0.034513334156404715 0.2662677325807121
chr12 133851895 4698685 0.03510361209305255 0.2090353867197467
chr13 115169878 3304044 0.02868843882946546 0.18661773010863636
chr14 107349540 3118364 0.029048694572887782 0.19454130148331686
chr15 102531392 2996083 0.02922112868612961 0.19166223667152704
chr16 90354753 3036828 0.0336100525890431 0.22025628875100678
chr17 81195210 2864529 0.0352795318837158 0.2213530385653949
chr18 78077248 2774098 0.03553017135030169 0.47791864498960024
chr19 59128983 2171276 0.03672101040533709 0.40554754849365693
chr20 63025520 2181044 0.03460572796543369 0.20912898480450118
chr21 48129895 1381854 0.028710929039009955 0.21672967874358082
chr22 51304566 1249042 0.024345630367480352 0.17259784038360984
chrMT 16571 64746 3.9071872548427975 2.773767922077943
chrX 155270560 5816378 0.03745963175504745 0.23540354772983
chrY 59373566 341441 0.005750724152226262 0.19822167001658952