BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6231832.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 = 3,338,269
number of mapped reads = 2,961,879 (88.72%)
number of supplementary alignments = 24,028 (0.72%)
number of secondary alignments = 0
number of mapped bases = 184,408,887 bp
number of sequenced bases = 184,339,263 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 764,973
duplication rate = 17.42%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.0741
>>>>>>> ACTG content
number of A's = 46,288,240 bp (25.11%)
number of C's = 33,118,749 bp (17.97%)
number of T's = 60,868,647 bp (33.02%)
number of G's = 43,993,344 bp (23.87%)
number of N's = 70,283 bp (0.04%)
GC percentage = 41.83%
>>>>>>> Mismatches and indels
general error rate = 0.0068
number of mismatches = 1,222,131
number of insertions = 12,174
mapped reads with insertion percentage = 0.41%
number of deletions = 39,744
mapped reads with deletion percentage = 1.33%
homopolymer indels = 42.81%
>>>>>>> Coverage
mean coverageData = 0.0596X
std coverageData = 0.7769X
There is a 2.78% of reference with a coverageData >= 1X
There is a 1.29% of reference with a coverageData >= 2X
There is a 0.71% of reference with a coverageData >= 3X
There is a 0.41% of reference with a coverageData >= 4X
There is a 0.24% of reference with a coverageData >= 5X
There is a 0.15% of reference with a coverageData >= 6X
There is a 0.09% of reference with a coverageData >= 7X
There is a 0.06% of reference with a coverageData >= 8X
There is a 0.04% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% 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 14473198 0.058066848306869416 1.1530451085749074
chr2 243199373 16514111 0.06790359200473761 1.5622406647536315
chr3 198022430 13199062 0.06665437849641578 0.49097687590497324
chr4 191154276 11614683 0.060760780470325446 0.48612303062106993
chr5 180915260 9565434 0.052872455314162 0.43819762149851826
chr6 171115067 12068026 0.07052579420139549 0.7544971170353609
chr7 159138663 11403968 0.07166057440108065 0.8253272758731074
chr8 146364022 8741534 0.05972460909826596 0.6778515633629751
chr9 141213431 7549650 0.05346269081161267 0.5554923354757147
chr10 135534747 8639843 0.063746332149054 0.6140392425879007
chr11 135006516 8576401 0.06352583011622935 0.5796087375075831
chr12 133851895 6457242 0.04824169280532039 0.43264285838963784
chr13 115169878 5663173 0.04917234522033617 0.48322794723886847
chr14 107349540 6119241 0.057002955019648895 0.47763533865286983
chr15 102531392 4575661 0.04462692752674225 0.4646434343813793
chr16 90354753 5582617 0.061785537723732145 0.5089675910069084
chr17 81195210 4819515 0.059357134491061725 0.4807991858758982
chr18 78077248 4850810 0.06212834243338085 1.273810253027587
chr19 59128983 4511073 0.07629207828587209 0.8147568412686624
chr20 63025520 4891763 0.07761559127159919 0.5611587943324079
chr21 48129895 2557044 0.053127977943853814 0.46186212640183694
chr22 51304566 2382505 0.04643845929814512 0.41985164854729984
chrMT 16571 439535 26.524349767666404 17.046293935304934
chrX 155270560 8596536 0.055364880502781724 0.48029511210065406
chrY 59373566 616262 0.010379400152586421 0.2660631605853576