BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6013263.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,089,100
number of mapped reads = 1,845,587 (88.34%)
number of supplementary alignments = 14,366 (0.69%)
number of secondary alignments = 0
number of mapped bases = 124,578,421 bp
number of sequenced bases = 124,525,275 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 124,361
duplication rate = 5.28%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.717
>>>>>>> ACTG content
number of A's = 35,152,881 bp (28.23%)
number of C's = 22,602,157 bp (18.15%)
number of T's = 40,254,926 bp (32.33%)
number of G's = 26,488,720 bp (21.27%)
number of N's = 26,591 bp (0.02%)
GC percentage = 39.42%
>>>>>>> Mismatches and indels
general error rate = 0.0084
number of mismatches = 1,029,880
number of insertions = 9,169
mapped reads with insertion percentage = 0.49%
number of deletions = 31,582
mapped reads with deletion percentage = 1.69%
homopolymer indels = 46.24%
>>>>>>> Coverage
mean coverageData = 0.0402X
std coverageData = 0.4066X
There is a 2.94% of reference with a coverageData >= 1X
There is a 0.72% of reference with a coverageData >= 2X
There is a 0.2% of reference with a coverageData >= 3X
There is a 0.06% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% 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 2263163 0.009079869052763563 0.47860833399060576
chr2 243199373 16362524 0.06728028858857296 0.6715896156072847
chr3 198022430 8722845 0.04404978264330965 0.2694416379342462
chr4 191154276 6353494 0.03323751962524762 0.23798566829291515
chr5 180915260 6089078 0.03365707237742134 0.23849666694469718
chr6 171115067 12113178 0.07078966342572277 0.445085662367991
chr7 159138663 8412466 0.052862490116559545 0.5285769774096233
chr8 146364022 6738854 0.0460417383173578 0.514467590865183
chr9 141213431 3830736 0.027127277999498503 0.41451056015696824
chr10 135534747 2525630 0.018634557232766295 0.31624913475519273
chr11 135006516 6000882 0.04444883238080153 0.36244506796714204
chr12 133851895 2654114 0.019828736828865965 0.1861998699998487
chr13 115169878 2817770 0.02446620634607254 0.2033025368043245
chr14 107349540 6267771 0.05838656597876433 0.3252403394201774
chr15 102531392 1419292 0.013842511764592058 0.15045666358739382
chr16 90354753 2991655 0.03311010102589733 0.26864098498480016
chr17 81195210 2970864 0.03658915347346229 0.2524504543414091
chr18 78077248 7245739 0.09280218226953901 0.8572284802151939
chr19 59128983 1805444 0.030533993794549113 0.4174845480012041
chr20 63025520 3475947 0.055151421202078145 0.30929661129303876
chr21 48129895 1521436 0.03161103925117643 0.23200010084861158
chr22 51304566 2796177 0.05450152331470848 0.3031791368076411
chrMT 16571 123353 7.443908032104279 6.0046079275261075
chrX 155270560 8804203 0.05670233301148653 0.3368236457375867
chrY 59373566 271806 0.004577895826570363 0.09802730230151106