BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3085046.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 = 3,347,587
number of mapped reads = 3,057,985 (91.35%)
number of supplementary alignments = 21,086 (0.63%)
number of secondary alignments = 0
number of mapped bases = 204,687,693 bp
number of sequenced bases = 204,612,985 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 123,665
duplication rate = 3.22%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.1266
>>>>>>> ACTG content
number of A's = 59,176,867 bp (28.92%)
number of C's = 39,068,221 bp (19.09%)
number of T's = 63,056,334 bp (30.82%)
number of G's = 43,288,784 bp (21.16%)
number of N's = 22,779 bp (0.01%)
GC percentage = 40.25%
>>>>>>> Mismatches and indels
general error rate = 0.0091
number of mismatches = 1,831,427
number of insertions = 14,469
mapped reads with insertion percentage = 0.47%
number of deletions = 43,122
mapped reads with deletion percentage = 1.4%
homopolymer indels = 47.46%
>>>>>>> Coverage
mean coverageData = 0.0661X
std coverageData = 0.4548X
There is a 5.27% of reference with a coverageData >= 1X
There is a 0.95% of reference with a coverageData >= 2X
There is a 0.21% of reference with a coverageData >= 3X
There is a 0.06% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% 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 16427016 0.06590561714187264 0.6184135897979728
chr2 243199373 21681907 0.08915280797208305 0.5757883402496771
chr3 198022430 14099744 0.07120276223254103 0.32941392628897276
chr4 191154276 11957364 0.0625534738234158 0.31396627102718055
chr5 180915260 8949966 0.049470486900883875 0.2652254183386069
chr6 171115067 14468596 0.08455477506256068 0.40847652778520904
chr7 159138663 19271262 0.12109729739277751 0.5880942440963369
chr8 146364022 10616176 0.07253268839523964 0.7565830307914532
chr9 141213431 7693849 0.05448383305692785 0.4081323740801891
chr10 135534747 14445898 0.10658446132636379 0.6357243890111047
chr11 135006516 7785333 0.057666349970841406 0.5137438181044348
chr12 133851895 8039406 0.06006195130819777 0.30208894729183167
chr13 115169878 4526201 0.03930021528719515 0.2353904560002563
chr14 107349540 5211299 0.048545145139886024 0.28984749836013
chr15 102531392 3209869 0.03130620717604224 0.21469790711117545
chr16 90354753 5955148 0.06590851949979876 0.3237328627616719
chr17 81195210 3092742 0.03809020261170579 0.30975727329289926
chr18 78077248 4769871 0.061091689604633605 0.636333574433387
chr19 59128983 2521522 0.04264443377962378 0.43773007775157297
chr20 63025520 4557893 0.07231821332057237 0.32544550836583325
chr21 48129895 2135456 0.04436859876797986 0.27248414020170275
chr22 51304566 1081237 0.02107486885280347 0.16827704691843395
chrMT 16571 18114 1.0931144770985457 1.3781596164938619
chrX 155270560 11751313 0.07568281456574898 0.3829684514860909
chrY 59373566 420511 0.007082461578945755 0.15107989671144853