BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524775.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 = 1,419,720
number of mapped reads = 1,268,766 (89.37%)
number of supplementary alignments = 4,904 (0.35%)
number of secondary alignments = 0
number of mapped bases = 72,063,019 bp
number of sequenced bases = 72,039,680 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 45,479
duplication rate = 2.73%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.503
>>>>>>> ACTG content
number of A's = 17,899,045 bp (24.85%)
number of C's = 13,157,569 bp (18.26%)
number of T's = 23,500,547 bp (32.62%)
number of G's = 17,473,673 bp (24.26%)
number of N's = 8,846 bp (0.01%)
GC percentage = 42.52%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 375,705
number of insertions = 4,756
mapped reads with insertion percentage = 0.37%
number of deletions = 14,352
mapped reads with deletion percentage = 1.12%
homopolymer indels = 41.49%
>>>>>>> Coverage
mean coverageData = 0.0233X
std coverageData = 0.2203X
There is a 2.1% of reference with a coverageData >= 1X
There is a 0.16% 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 5770283 0.023150526072310166 0.28509072232409804
chr2 243199373 6093483 0.025055504563327967 0.36317161573265266
chr3 198022430 4747057 0.023972319701359084 0.17133649452686944
chr4 191154276 4635155 0.024248241247818072 0.19052138054834905
chr5 180915260 4304331 0.023791973103871947 0.1674376330455187
chr6 171115067 4093617 0.02392318263826528 0.18978107838446
chr7 159138663 3958746 0.02487607929695878 0.25938000924692356
chr8 146364022 3589570 0.024524947804454293 0.2015910892816832
chr9 141213431 3091406 0.021891727848465065 0.19011625600676646
chr10 135534747 3521401 0.025981536675609835 0.2611336181051953
chr11 135006516 3243475 0.02402458115429036 0.19821426862219912
chr12 133851895 3253582 0.024307328633636452 0.1713294889237371
chr13 115169878 2215841 0.019239761632811662 0.15117084032807607
chr14 107349540 2186040 0.02036375749723753 0.15839592118025245
chr15 102531392 2077161 0.020258780842456522 0.15630814904585333
chr16 90354753 2171287 0.024030689342928093 0.18788838735271707
chr17 81195210 2021798 0.024900459029541275 0.17842653679165485
chr18 78077248 1862213 0.02385090468352573 0.2775573963565351
chr19 59128983 1559146 0.026368557700375127 0.23952205529816392
chr20 63025520 1551838 0.024622375190240398 0.17667662719960583
chr21 48129895 954903 0.019840122235878555 0.1695037882621318
chr22 51304566 894638 0.017437785167113588 0.14450936441489182
chrMT 16571 28883 1.742984732363768 1.7606334920702982
chrX 155270560 4001776 0.02577292179534871 0.18634565507870135
chrY 59373566 235389 0.003964542065740165 0.11500809362416155