BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524694.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 = 2,714,963
number of mapped reads = 2,496,759 (91.96%)
number of supplementary alignments = 10,270 (0.38%)
number of secondary alignments = 0
number of mapped bases = 147,275,477 bp
number of sequenced bases = 147,230,583 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 125,123
duplication rate = 3.64%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6674
>>>>>>> ACTG content
number of A's = 36,968,875 bp (25.11%)
number of C's = 29,884,760 bp (20.3%)
number of T's = 47,301,924 bp (32.13%)
number of G's = 33,055,749 bp (22.45%)
number of N's = 19,275 bp (0.01%)
GC percentage = 42.75%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 740,660
number of insertions = 13,067
mapped reads with insertion percentage = 0.52%
number of deletions = 28,164
mapped reads with deletion percentage = 1.12%
homopolymer indels = 42.06%
>>>>>>> Coverage
mean coverageData = 0.0476X
std coverageData = 0.4226X
There is a 4.11% of reference with a coverageData >= 1X
There is a 0.46% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% 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 11771202 0.047226369799094704 0.7794464749462958
chr2 243199373 12474525 0.05129340937897895 0.6216047424628074
chr3 198022430 9779891 0.0493877940998906 0.2529118676024372
chr4 191154276 9477533 0.04958054404181887 0.29339786419135905
chr5 180915260 8853839 0.04893914974336604 0.2536827444140901
chr6 171115067 8533370 0.049869191238431386 0.3053629261928112
chr7 159138663 8122578 0.05104088376059814 0.5241428837215568
chr8 146364022 7531086 0.05145448927332702 0.4416519274299626
chr9 141213431 6196357 0.043879374335150885 0.3409897036329537
chr10 135534747 7058196 0.05207665308144191 0.4397258446047413
chr11 135006516 6691466 0.04956402252466096 0.3481139193122595
chr12 133851895 6666743 0.049806863025734525 0.2565251470316784
chr13 115169878 4639151 0.040280940472994166 0.2291221944464666
chr14 107349540 4412232 0.04110154547471745 0.2408581533496127
chr15 102531392 4202030 0.04098286308255719 0.23481335058223265
chr16 90354753 4265831 0.04721202657706341 0.27922617692993756
chr17 81195210 3998028 0.049239702686894954 0.2787319662330702
chr18 78077248 3916636 0.050163602077778154 0.6417037497929915
chr19 59128983 3055148 0.05166921271079531 0.5712938317823165
chr20 63025520 3102068 0.04921923690593905 0.2585659565850846
chr21 48129895 1927377 0.0400453190267712 0.26634738750065196
chr22 51304566 1775181 0.03460083845168869 0.21210147589926057
chrMT 16571 40801 2.4621929877496833 2.1150695378932274
chrX 155270560 8308967 0.05351282947649574 0.2978543431609759
chrY 59373566 475241 0.008004252262698859 0.25753006121563227