BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6013243.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 = 1,744,028
number of mapped reads = 1,536,185 (88.08%)
number of supplementary alignments = 18,342 (1.05%)
number of secondary alignments = 0
number of mapped bases = 99,668,324 bp
number of sequenced bases = 99,593,799 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 107,954
duplication rate = 5.81%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9816
>>>>>>> ACTG content
number of A's = 28,196,486 bp (28.31%)
number of C's = 17,688,067 bp (17.76%)
number of T's = 32,460,493 bp (32.59%)
number of G's = 21,227,741 bp (21.31%)
number of N's = 21,012 bp (0.02%)
GC percentage = 39.07%
>>>>>>> Mismatches and indels
general error rate = 0.0094
number of mismatches = 918,106
number of insertions = 7,672
mapped reads with insertion percentage = 0.5%
number of deletions = 42,844
mapped reads with deletion percentage = 2.74%
homopolymer indels = 43.85%
>>>>>>> Coverage
mean coverageData = 0.0322X
std coverageData = 0.3317X
There is a 2.31% of reference with a coverageData >= 1X
There is a 0.61% of reference with a coverageData >= 2X
There is a 0.18% of reference with a coverageData >= 3X
There is a 0.05% 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% 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 6379069 0.025592991401213 0.5750148288735293
chr2 243199373 9020326 0.03709025187330561 0.383889369629702
chr3 198022430 4664559 0.02355571033039035 0.20148819378691768
chr4 191154276 4635830 0.024251772427000273 0.23857882581515125
chr5 180915260 7035735 0.03888967133010228 0.26244300348279914
chr6 171115067 3528387 0.02061996679696242 0.199929485807518
chr7 159138663 3735260 0.023471731693510585 0.30289466926534453
chr8 146364022 7084838 0.04840559792761093 0.5137627015373408
chr9 141213431 4665169 0.033036298084139035 0.291639803560143
chr10 135534747 4060132 0.02995639192066371 0.32599190882899143
chr11 135006516 6158201 0.04561410206304413 0.3239497011880144
chr12 133851895 2716344 0.02029365366848187 0.1885093051109559
chr13 115169878 3197904 0.0277668436880692 0.2217552125438702
chr14 107349540 4379544 0.04079704486856674 0.2834378558042413
chr15 102531392 2014971 0.019652234897971542 0.18348736640131613
chr16 90354753 4077279 0.04512522988137658 0.2883799649787318
chr17 81195210 3234517 0.03983630315138048 0.28643197635238066
chr18 78077248 1884834 0.024140630571405385 0.38390092662915826
chr19 59128983 2585580 0.04372779420204132 0.47855737251318825
chr20 63025520 2507708 0.03978877127868203 0.2652729560528441
chr21 48129895 1630924 0.033885883191725225 0.2595074288956106
chr22 51304566 818937 0.015962263475730407 0.16095865081319058
chrMT 16571 8605 0.5192806710518375 0.9748706803146857
chrX 155270560 9383431 0.060432776181138265 0.33987201579981435
chrY 59373566 260240 0.0043830953323571635 0.14010792521010762