BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716341.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 = 1,361,140
number of mapped reads = 1,207,946 (88.75%)
number of supplementary alignments = 6,967 (0.51%)
number of secondary alignments = 0
number of mapped bases = 70,487,310 bp
number of sequenced bases = 70,466,735 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 34,244
duplication rate = 2.14%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.8781
>>>>>>> ACTG content
number of A's = 18,127,550 bp (25.72%)
number of C's = 14,243,511 bp (20.21%)
number of T's = 21,511,347 bp (30.53%)
number of G's = 16,583,485 bp (23.53%)
number of N's = 842 bp (0%)
GC percentage = 43.75%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 346,824
number of insertions = 5,051
mapped reads with insertion percentage = 0.42%
number of deletions = 12,821
mapped reads with deletion percentage = 1.05%
homopolymer indels = 42.14%
>>>>>>> Coverage
mean coverageData = 0.0228X
std coverageData = 0.2074X
There is a 2.08% of reference with a coverageData >= 1X
There is a 0.14% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 5696310 0.022853744464692828 0.30907884221333326
chr2 243199373 5946392 0.024450688036930096 0.2633355781628851
chr3 198022430 4672521 0.023595917896775634 0.16442585626818104
chr4 191154276 4483841 0.023456660734076387 0.17780424255943442
chr5 180915260 4204485 0.023240079360911842 0.16379404272661383
chr6 171115067 4075360 0.023816488351665725 0.17853592919322075
chr7 159138663 3868777 0.024310729567961747 0.2692517570615838
chr8 146364022 3568322 0.024379775516144262 0.20179944452092027
chr9 141213431 2930712 0.020753776600754073 0.17857706955837557
chr10 135534747 3367527 0.024846226333384458 0.21537743934155815
chr11 135006516 3218683 0.02384094557332329 0.19879561094013182
chr12 133851895 3229632 0.024128399526954773 0.16765627074251624
chr13 115169878 2185476 0.018976107624252236 0.147211551875526
chr14 107349540 2106035 0.019618481830476403 0.15433350092838038
chr15 102531392 2069845 0.020187427085745602 0.15713671328730622
chr16 90354753 2117544 0.023435889421334594 0.17289916990767554
chr17 81195210 2007635 0.024726027557536952 0.1770997953296582
chr18 78077248 1850940 0.023706522033153626 0.2912189657980282
chr19 59128983 1511950 0.02557037045605875 0.2675740622537063
chr20 63025520 1499231 0.02378768156137387 0.16868073792107507
chr21 48129895 918116 0.019075794784094168 0.162250791766235
chr22 51304566 896890 0.01748167989570363 0.1418307484813087
chrMT 16571 17784 1.0732001689698871 1.2899427748090795
chrX 155270560 3832196 0.02468076369403189 0.17857683861289161
chrY 59373566 211106 0.0035555553459598504 0.09402528761940757