BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472384.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 21,759,060
number of mapped reads = 21,579,527 (99.17%)
number of supplementary alignments = 82,407 (0.38%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 10,830,604
number of mapped paired reads (second in pair) = 10,748,923
number of mapped paired reads (both in pair) = 21,457,634
number of mapped paired reads (singletons) = 121,893
number of mapped bases = 2,118,476,300 bp
number of sequenced bases = 2,118,216,664 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 13,783,826
duplication rate = 49.02%
>>>>>>> Insert size
mean insert size = 20,369.9483
std insert size = 1,394,624.375
median insert size = 225
>>>>>>> Mapping quality
mean mapping quality = 54.8895
>>>>>>> ACTG content
number of A's = 576,997,775 bp (27.24%)
number of C's = 483,973,013 bp (22.85%)
number of T's = 577,186,275 bp (27.25%)
number of G's = 479,796,038 bp (22.65%)
number of N's = 263,563 bp (0.01%)
GC percentage = 45.5%
>>>>>>> Mismatches and indels
general error rate = 0.0056
number of mismatches = 11,572,756
number of insertions = 126,447
mapped reads with insertion percentage = 0.58%
number of deletions = 108,882
mapped reads with deletion percentage = 0.49%
homopolymer indels = 46.37%
>>>>>>> Coverage
mean coverageData = 0.6843X
std coverageData = 19.3865X
There is a 5.7% of reference with a coverageData >= 1X
There is a 2.45% of reference with a coverageData >= 2X
There is a 1.03% of reference with a coverageData >= 3X
There is a 0.76% of reference with a coverageData >= 4X
There is a 0.57% of reference with a coverageData >= 5X
There is a 0.52% of reference with a coverageData >= 6X
There is a 0.48% of reference with a coverageData >= 7X
There is a 0.46% of reference with a coverageData >= 8X
There is a 0.44% of reference with a coverageData >= 9X
There is a 0.42% of reference with a coverageData >= 10X
There is a 0.41% of reference with a coverageData >= 11X
There is a 0.4% of reference with a coverageData >= 12X
There is a 0.39% of reference with a coverageData >= 13X
There is a 0.38% of reference with a coverageData >= 14X
There is a 0.37% of reference with a coverageData >= 15X
There is a 0.36% of reference with a coverageData >= 16X
There is a 0.35% of reference with a coverageData >= 17X
There is a 0.35% of reference with a coverageData >= 18X
There is a 0.34% of reference with a coverageData >= 19X
There is a 0.33% of reference with a coverageData >= 20X
There is a 0.33% of reference with a coverageData >= 21X
There is a 0.32% of reference with a coverageData >= 22X
There is a 0.31% of reference with a coverageData >= 23X
There is a 0.31% of reference with a coverageData >= 24X
There is a 0.3% of reference with a coverageData >= 25X
There is a 0.3% of reference with a coverageData >= 26X
There is a 0.29% of reference with a coverageData >= 27X
There is a 0.29% of reference with a coverageData >= 28X
There is a 0.29% of reference with a coverageData >= 29X
There is a 0.28% of reference with a coverageData >= 30X
There is a 0.28% of reference with a coverageData >= 31X
There is a 0.27% of reference with a coverageData >= 32X
There is a 0.27% of reference with a coverageData >= 33X
There is a 0.27% of reference with a coverageData >= 34X
There is a 0.26% of reference with a coverageData >= 35X
There is a 0.26% of reference with a coverageData >= 36X
There is a 0.26% of reference with a coverageData >= 37X
There is a 0.25% of reference with a coverageData >= 38X
There is a 0.25% of reference with a coverageData >= 39X
There is a 0.25% of reference with a coverageData >= 40X
There is a 0.24% of reference with a coverageData >= 41X
There is a 0.24% of reference with a coverageData >= 42X
There is a 0.24% of reference with a coverageData >= 43X
There is a 0.24% of reference with a coverageData >= 44X
There is a 0.23% of reference with a coverageData >= 45X
There is a 0.23% of reference with a coverageData >= 46X
There is a 0.23% of reference with a coverageData >= 47X
There is a 0.23% of reference with a coverageData >= 48X
There is a 0.22% of reference with a coverageData >= 49X
There is a 0.22% of reference with a coverageData >= 50X
There is a 0.22% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 170330211 0.6833692542735932 19.246131756920168
chr2 243199373 160712596 0.6608265227723263 17.1733243161596
chr3 198022430 172202108 0.8696091043827712 20.17919529590582
chr4 191154276 58523761 0.30615983186272017 11.941400735374579
chr5 180915260 83441474 0.46121855060761596 15.229945129014439
chr6 171115067 184440625 1.077874837287122 26.941059396202984
chr7 159138663 165874579 1.0423273381403235 25.140659491558274
chr8 146364022 110541340 0.7552494013863599 20.473795498949023
chr9 141213431 76635385 0.5426918987613862 19.311031385121318
chr10 135534747 51959128 0.3833638911798758 15.065851949076759
chr11 135006516 62623947 0.4638586999756367 14.07781235981556
chr12 133851895 104801479 0.7829659714567359 17.254554388066182
chr13 115169878 55778513 0.48431511753446504 15.396132096444118
chr14 107349540 40536513 0.3776123586556589 11.222496751222407
chr15 102531392 42466405 0.4141795422030357 11.424927225300623
chr16 90354753 107399721 1.1886449515278958 32.14165254063896
chr17 81195210 103378061 1.2732039365376357 29.445221130375717
chr18 78077248 28253628 0.36186762115386034 11.113714377878944
chr19 59128983 51082871 0.8639227060610868 17.071087336208095
chr20 63025520 76083753 1.207189611446284 28.061151538356558
chr21 48129895 15373652 0.3194200195117816 13.339801181109916
chr22 51304566 17777488 0.34650888577831457 9.944567061879201
chrMT 16571 4469 0.269688009172651 0.7619173385064547
chrX 155270560 177773432 1.1449268425385983 26.00588558288828
chrY 59373566 481161 0.008103959933954448 0.568443237365562