BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3080789.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,755,401
number of mapped reads = 1,583,763 (90.22%)
number of supplementary alignments = 16,195 (0.92%)
number of secondary alignments = 0
number of mapped bases = 103,704,045 bp
number of sequenced bases = 103,668,464 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 57,214
duplication rate = 3.03%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.3953
>>>>>>> ACTG content
number of A's = 30,203,321 bp (29.13%)
number of C's = 19,601,565 bp (18.91%)
number of T's = 32,000,519 bp (30.87%)
number of G's = 21,860,962 bp (21.09%)
number of N's = 2,097 bp (0%)
GC percentage = 40%
>>>>>>> Mismatches and indels
general error rate = 0.0076
number of mismatches = 776,484
number of insertions = 7,866
mapped reads with insertion percentage = 0.49%
number of deletions = 22,510
mapped reads with deletion percentage = 1.41%
homopolymer indels = 47.23%
>>>>>>> Coverage
mean coverageData = 0.0335X
std coverageData = 0.2696X
There is a 2.84% of reference with a coverageData >= 1X
There is a 0.39% 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% 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 13335932 0.053504107418051325 0.42109188645982204
chr2 243199373 7856035 0.03230285877422883 0.28453456429458834
chr3 198022430 6331607 0.03197419100452408 0.20498156158233347
chr4 191154276 6241770 0.03265304930976276 0.21328024864557452
chr5 180915260 7976426 0.04408929351786024 0.24159684257787764
chr6 171115067 7630687 0.044593893067289045 0.2696880059789612
chr7 159138663 7036034 0.04421322805759654 0.3402772445358029
chr8 146364022 4540252 0.031020273547825845 0.42356232031500046
chr9 141213431 3675595 0.0260286502067923 0.22064907876705242
chr10 135534747 4011666 0.02959880096282616 0.2422476870324884
chr11 135006516 4199561 0.031106357859053264 0.22114805427156034
chr12 133851895 4012693 0.0299786043372789 0.2005639415107386
chr13 115169878 4505406 0.0391196559225321 0.22837646756081886
chr14 107349540 2706191 0.025209153201774318 0.18826268708849922
chr15 102531392 2631289 0.025663252479786874 0.18979557737427652
chr16 90354753 2199712 0.024345282643847194 0.1862680627971993
chr17 81195210 2627742 0.03236326379351688 0.21250156721105173
chr18 78077248 1337269 0.01712751197378268 0.3610502057421231
chr19 59128983 1323445 0.022382339976995715 0.2938062550122169
chr20 63025520 1639443 0.026012367688517286 0.18650328491938672
chr21 48129895 1630897 0.03388532220982406 0.21651161702499788
chr22 51304566 870514 0.016967573607386134 0.14713878605306374
chrMT 16571 44184 2.666344819262567 2.1612646555205437
chrX 155270560 5103846 0.03287066137972324 0.21778155646857794
chrY 59373566 235849 0.003972289621276917 0.0954573784446051