BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716482.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 644,510
number of mapped reads = 561,115 (87.06%)
number of supplementary alignments = 1,632 (0.25%)
number of secondary alignments = 0
number of mapped bases = 31,537,995 bp
number of sequenced bases = 31,528,285 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 9,372
duplication rate = 1.16%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 39.99
>>>>>>> ACTG content
number of A's = 6,945,201 bp (22.03%)
number of C's = 6,505,384 bp (20.63%)
number of T's = 9,591,619 bp (30.42%)
number of G's = 8,485,249 bp (26.91%)
number of N's = 832 bp (0%)
GC percentage = 47.55%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 166,631
number of insertions = 2,073
mapped reads with insertion percentage = 0.37%
number of deletions = 5,678
mapped reads with deletion percentage = 1%
homopolymer indels = 39.16%
>>>>>>> Coverage
mean coverageData = 0.0102X
std coverageData = 0.119X
There is a 0.96% of reference with a coverageData >= 1X
There is a 0.04% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% 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 2980533 0.011957976225062244 0.14405037809639973
chr2 243199373 2648962 0.010892141568144586 0.15101894621676845
chr3 198022430 2014983 0.010175529105465477 0.10944543500682247
chr4 191154276 1982995 0.010373793573940245 0.11756161694264368
chr5 180915260 2575396 0.014235371853098517 0.12511229428698098
chr6 171115067 1267371 0.007406542405760213 0.09194245551698496
chr7 159138663 1746637 0.010975566635243128 0.1256416842053371
chr8 146364022 1865690 0.012746916725204505 0.12181375026532641
chr9 141213431 1336049 0.009461203446009325 0.10707485473459688
chr10 135534747 1581192 0.011666321994905115 0.15611997091107455
chr11 135006516 1284672 0.009515629601166807 0.11324977302732961
chr12 133851895 1474086 0.01101281382680462 0.10981087301515702
chr13 115169878 538846 0.004678706006791116 0.07204375078867593
chr14 107349540 1360475 0.012673319326752587 0.11936566789568692
chr15 102531392 611485 0.005963880798575328 0.08092132214963424
chr16 90354753 823052 0.009109116816466756 0.10652937658622476
chr17 81195210 1199259 0.01477007079604819 0.1302128689887358
chr18 78077248 813780 0.01042275465446733 0.12533980515150625
chr19 59128983 838732 0.014184786503092739 0.14238675199041914
chr20 63025520 781637 0.012401912748994376 0.11944184707833161
chr21 48129895 406103 0.008437645667001767 0.10222038930988675
chr22 51304566 345595 0.0067361450830711635 0.08712138415576609
chrMT 16571 13120 0.791744614084847 1.0809954447003354
chrX 155270560 944670 0.0060840252009138115 0.0861105362323395
chrY 59373566 102675 0.0017293049233391168 0.06669548306618546