BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716746.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 = 1,731,561
number of mapped reads = 1,278,401 (73.83%)
number of supplementary alignments = 1,375 (0.08%)
number of secondary alignments = 0
number of mapped bases = 66,459,578 bp
number of sequenced bases = 66,443,776 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 132,857
duplication rate = 8.91%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.7632
>>>>>>> ACTG content
number of A's = 13,372,445 bp (20.13%)
number of C's = 11,438,193 bp (17.21%)
number of T's = 22,392,200 bp (33.7%)
number of G's = 19,239,798 bp (28.96%)
number of N's = 1,140 bp (0%)
GC percentage = 46.17%
>>>>>>> Mismatches and indels
general error rate = 0.0067
number of mismatches = 438,334
number of insertions = 3,511
mapped reads with insertion percentage = 0.27%
number of deletions = 9,263
mapped reads with deletion percentage = 0.72%
homopolymer indels = 42.28%
>>>>>>> Coverage
mean coverageData = 0.0215X
std coverageData = 0.2014X
There is a 1.76% of reference with a coverageData >= 1X
There is a 0.28% of reference with a coverageData >= 2X
There is a 0.06% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% 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 6283460 0.025209405596626377 0.22292092073150405
chr2 243199373 5578581 0.022938303381234457 0.31347395525644184
chr3 198022430 4310714 0.021768816795147902 0.18084930890032094
chr4 191154276 4081288 0.021350754403213035 0.17944685838779414
chr5 180915260 5610751 0.03101314394374471 0.2133624318780893
chr6 171115067 2785043 0.0162758490460691 0.1777707494172625
chr7 159138663 3482964 0.02188634700292788 0.18783260409261582
chr8 146364022 4003023 0.027349774523140667 0.20896919574450343
chr9 141213431 2850883 0.020188469183218132 0.18318171103912176
chr10 135534747 3299855 0.02434693001640384 0.20396848616789418
chr11 135006516 2705005 0.020036106997976304 0.1900886963243077
chr12 133851895 3028723 0.022627419656628695 0.1847124612612688
chr13 115169878 1090940 0.009472442091151646 0.11856949522691461
chr14 107349540 2914499 0.027149617967622403 0.2018345155167652
chr15 102531392 1152433 0.011239806438987974 0.1293916081469259
chr16 90354753 1659968 0.01837167326438267 0.17534056312071405
chr17 81195210 2638103 0.0324908698431841 0.22993590350828857
chr18 78077248 1687441 0.021612454885704988 0.19431785719871475
chr19 59128983 1764906 0.029848407844254653 0.26100667366903807
chr20 63025520 1708230 0.027103782721665762 0.21211929972296023
chr21 48129895 884876 0.018385163732436982 0.1726704923038458
chr22 51304566 731655 0.014261011388343096 0.17375735499369593
chrMT 16571 3543 0.2138072536358699 0.5947139319418857
chrX 155270560 2029038 0.013067757339189091 0.14198603978394952
chrY 59373566 173656 0.002924803270196033 0.07832662433347921