BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716890.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 = 10,806,500
number of mapped reads = 9,497,571 (87.89%)
number of supplementary alignments = 54,741 (0.51%)
number of secondary alignments = 0
number of mapped bases = 544,138,455 bp
number of sequenced bases = 543,975,814 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 729,100
duplication rate = 5.41%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.2539
>>>>>>> ACTG content
number of A's = 137,921,187 bp (25.35%)
number of C's = 108,760,674 bp (19.99%)
number of T's = 167,351,651 bp (30.76%)
number of G's = 129,934,309 bp (23.89%)
number of N's = 7,993 bp (0%)
GC percentage = 43.88%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 2,758,275
number of insertions = 31,187
mapped reads with insertion percentage = 0.33%
number of deletions = 102,737
mapped reads with deletion percentage = 1.07%
homopolymer indels = 41.64%
>>>>>>> Coverage
mean coverageData = 0.1758X
std coverageData = 1.2716X
There is a 11.95% of reference with a coverageData >= 1X
There is a 3.29% of reference with a coverageData >= 2X
There is a 1.1% of reference with a coverageData >= 3X
There is a 0.43% of reference with a coverageData >= 4X
There is a 0.19% of reference with a coverageData >= 5X
There is a 0.1% of reference with a coverageData >= 6X
There is a 0.06% of reference with a coverageData >= 7X
There is a 0.04% of reference with a coverageData >= 8X
There is a 0.03% of reference with a coverageData >= 9X
There is a 0.02% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% 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 42089008 0.16886219914372852 1.821526517050751
chr2 243199373 55994488 0.2302410870113551 1.7533361226879678
chr3 198022430 39355200 0.19874112240719397 0.74535094757939
chr4 191154276 32426283 0.16963409701596213 0.6584592195900567
chr5 180915260 30940105 0.17101987416650205 0.5841902558810668
chr6 171115067 32450735 0.18964276827826038 0.8247423224838848
chr7 159138663 27904171 0.175345013423922 2.9397987166961834
chr8 146364022 46883310 0.3203199075794733 1.277175409887826
chr9 141213431 21462086 0.1519833194903394 0.8375891892845022
chr10 135534747 26762353 0.19745750512228424 1.8713459093465188
chr11 135006516 18979999 0.14058579957725892 0.8106072350131444
chr12 133851895 27418645 0.20484315892576643 0.7670093538249901
chr13 115169878 15059279 0.13075709778905906 0.5021866879888253
chr14 107349540 6197690 0.05773373598061063 0.45749938989944167
chr15 102531392 13420496 0.13089158099014203 0.5343733234028899
chr16 90354753 16960316 0.1877080666691657 0.7306543222398278
chr17 81195210 21023207 0.2589217639809048 0.8110394509862897
chr18 78077248 12371185 0.15844801548333262 1.4769639368672778
chr19 59128983 11136795 0.1883474809637771 1.7592530832262365
chr20 63025520 12406809 0.19685373480456805 0.6990925829442246
chr21 48129895 5800213 0.12051164873723494 0.551132369221631
chr22 51304566 5380473 0.10487318029354346 0.4517360805704929
chrMT 16571 33835 2.041820047070183 2.542089564425396
chrX 155270560 20520894 0.1321621690550997 0.7822178246126529
chrY 59373566 1160880 0.019552135372835785 0.38557849513739295