BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3083773.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 = 2,074,692
number of mapped reads = 1,211,729 (58.41%)
number of supplementary alignments = 8,511 (0.41%)
number of secondary alignments = 0
number of mapped bases = 77,096,186 bp
number of sequenced bases = 77,069,605 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 35,144
duplication rate = 2.45%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.8623
>>>>>>> ACTG content
number of A's = 21,741,747 bp (28.21%)
number of C's = 14,459,585 bp (18.76%)
number of T's = 23,711,772 bp (30.77%)
number of G's = 17,155,626 bp (22.26%)
number of N's = 875 bp (0%)
GC percentage = 41.02%
>>>>>>> Mismatches and indels
general error rate = 0.0084
number of mismatches = 640,556
number of insertions = 5,697
mapped reads with insertion percentage = 0.47%
number of deletions = 16,623
mapped reads with deletion percentage = 1.36%
homopolymer indels = 46.81%
>>>>>>> Coverage
mean coverageData = 0.0249X
std coverageData = 0.2034X
There is a 2.27% of reference with a coverageData >= 1X
There is a 0.17% of reference with a coverageData >= 2X
There is a 0.02% 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 6232640 0.02500551442959093 0.2773577887007018
chr2 243199373 6584945 0.027076323917989708 0.24701130291379947
chr3 198022430 5371510 0.027125765500403163 0.17689096064189713
chr4 191154276 5310279 0.027780069120713784 0.18355210790340817
chr5 180915260 4802162 0.026543708916539156 0.17462037334489508
chr6 171115067 4637787 0.027103323402842137 0.1901849930514341
chr7 159138663 4134729 0.02598192621487589 0.21784740510441464
chr8 146364022 4032662 0.027552276474064098 0.21766848848203113
chr9 141213431 3079341 0.02180628979972875 0.1894380220970825
chr10 135534747 3561404 0.026276686081097712 0.21956951073525363
chr11 135006516 3362507 0.024906257117249066 0.18488950996211864
chr12 133851895 3470377 0.025926991918941454 0.1733696204886445
chr13 115169878 2587361 0.022465605112475678 0.16079828153681905
chr14 107349540 2288712 0.02132018451127038 0.1612183078275731
chr15 102531392 2182478 0.021285949185201738 0.15812783060949065
chr16 90354753 2062971 0.02283190348602912 0.17172648248334302
chr17 81195210 1931022 0.02378246204425113 0.17360584942968119
chr18 78077248 2024313 0.02592705367894114 0.32033729890019136
chr19 59128983 1333319 0.022549330841695688 0.23549460393313074
chr20 63025520 1454581 0.023079238378358482 0.16688492830030519
chr21 48129895 998673 0.02074953622899032 0.1605348031782582
chr22 51304566 793424 0.015464978302321084 0.133042684437655
chrMT 16571 6757 0.40776054553134994 0.692109288526588
chrX 155270560 4648108 0.0299355396154944 0.19524225683679292
chrY 59373566 204124 0.0034379609269215867 0.08140104762167855