BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6008673.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 = 1,634,916
number of mapped reads = 1,468,744 (89.84%)
number of supplementary alignments = 13,673 (0.84%)
number of secondary alignments = 0
number of mapped bases = 97,280,207 bp
number of sequenced bases = 97,231,493 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 56,262
duplication rate = 2.81%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.1457
>>>>>>> ACTG content
number of A's = 27,128,250 bp (27.9%)
number of C's = 18,009,854 bp (18.52%)
number of T's = 30,702,484 bp (31.58%)
number of G's = 21,250,975 bp (21.86%)
number of N's = 139,930 bp (0.14%)
GC percentage = 40.38%
>>>>>>> Mismatches and indels
general error rate = 0.0085
number of mismatches = 812,533
number of insertions = 7,134
mapped reads with insertion percentage = 0.48%
number of deletions = 27,743
mapped reads with deletion percentage = 1.87%
homopolymer indels = 46.35%
>>>>>>> Coverage
mean coverageData = 0.0314X
std coverageData = 0.3499X
There is a 2.67% of reference with a coverageData >= 1X
There is a 0.34% of reference with a coverageData >= 2X
There is a 0.05% 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 8959624 0.0359462454458639 0.7133014524567634
chr2 243199373 8989362 0.036962932466112895 0.35713251866438306
chr3 198022430 5727164 0.028921794364406093 0.20082881439338718
chr4 191154276 6228028 0.0325811597329897 0.21401885678985827
chr5 180915260 5342944 0.029532854221363085 0.19605824245510153
chr6 171115067 5729899 0.03348564857821667 0.23876888279809352
chr7 159138663 5320306 0.03343188826463874 0.3418303257858752
chr8 146364022 5836184 0.039874444007831376 0.6056201268337941
chr9 141213431 3861804 0.027347285400919123 0.2680835391334491
chr10 135534747 3943142 0.029093218434974463 0.4143663396575005
chr11 135006516 4544509 0.03366140490581951 0.2602389391349047
chr12 133851895 4799362 0.03585576431323591 0.21838855522223855
chr13 115169878 2477934 0.02151546952233465 0.165734877579476
chr14 107349540 3418886 0.03184816627998592 0.21555241827020705
chr15 102531392 2389969 0.02330963184426483 0.1736439904996594
chr16 90354753 2495062 0.027614064752077845 0.2253163349784083
chr17 81195210 2430836 0.02993816999795924 0.2171604747865606
chr18 78077248 2920317 0.03740291922174306 0.4848737566125
chr19 59128983 1680309 0.02841768815810683 0.4669726637374823
chr20 63025520 1686096 0.026752591648589334 0.19313886424922344
chr21 48129895 1264255 0.02626756197992952 0.19649712677361242
chr22 51304566 889990 0.01734718894220838 0.14657587756444213
chrMT 16571 5949 0.35900066381027096 0.6507318937976488
chrX 155270560 6071943 0.039105565150277036 0.24377980744203517
chrY 59373566 266333 0.004485716758195053 0.12488318414862169