BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR053607.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 6,268,603
number of mapped reads = 3,889,516 (62.05%)
number of supplementary alignments = 95 (0%)
number of secondary alignments = 0
number of mapped bases = 181,918,544 bp
number of sequenced bases = 181,881,682 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 712,601
duplication rate = 13.97%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.4202
>>>>>>> ACTG content
number of A's = 54,579,134 bp (30.01%)
number of C's = 35,491,110 bp (19.51%)
number of T's = 53,729,604 bp (29.54%)
number of G's = 37,988,249 bp (20.89%)
number of N's = 93,585 bp (0.05%)
GC percentage = 40.4%
>>>>>>> Mismatches and indels
general error rate = 0.0083
number of mismatches = 1,503,596
number of insertions = 9,727
mapped reads with insertion percentage = 0.25%
number of deletions = 25,597
mapped reads with deletion percentage = 0.66%
homopolymer indels = 45.08%
>>>>>>> Coverage
mean coverageData = 0.0588X
std coverageData = 0.78X
There is a 3.2% of reference with a coverageData >= 1X
There is a 1.13% of reference with a coverageData >= 2X
There is a 0.56% of reference with a coverageData >= 3X
There is a 0.31% of reference with a coverageData >= 4X
There is a 0.19% of reference with a coverageData >= 5X
There is a 0.12% of reference with a coverageData >= 6X
There is a 0.08% of reference with a coverageData >= 7X
There is a 0.06% of reference with a coverageData >= 8X
There is a 0.04% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.02% 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% 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 14460203 0.05801471202753794 0.5150409117080226
chr2 243199373 15824307 0.06506721956063595 2.2117839251918148
chr3 198022430 12344142 0.06233708979331281 0.47185172519728147
chr4 191154276 12136710 0.06349170028506189 0.49528022437612823
chr5 180915260 11252293 0.06219648359126809 0.47043010230079696
chr6 171115067 10752083 0.06283539602038668 0.5064478833950132
chr7 159138663 9764116 0.06135602634791521 0.5489664799214541
chr8 146364022 9378307 0.06407522061671686 0.5166799143051405
chr9 141213431 7548868 0.053457153094736434 0.45072935271958525
chr10 135534747 8346102 0.06157905765670555 0.5006304911426536
chr11 135006516 8325473 0.061667193900478104 0.5131206991370341
chr12 133851895 8293417 0.0619596532421151 0.4668307552798356
chr13 115169878 5955552 0.05171102117517221 0.43237682904084457
chr14 107349540 5543196 0.05163688638069618 0.4812977033528688
chr15 102531392 5200171 0.05071784259010158 0.4207451377548155
chr16 90354753 5050071 0.055891592111374594 0.45617988118240227
chr17 81195210 4511831 0.05556769912904961 0.4379627439594921
chr18 78077248 4699119 0.06018551012453718 0.5118356614924376
chr19 59128983 3205160 0.05420624264753547 0.4777414051029767
chr20 63025520 3757860 0.05962441880685792 0.4591709149185563
chr21 48129895 2249575 0.04673966149313228 0.42319945518738583
chr22 51304566 1888500 0.03680958922837394 0.34941167645438204
chrMT 16571 19098 1.152495323154909 3.011924376581598
chrX 155270560 10949451 0.07051852585577073 0.6962834855244187
chrY 59373566 462939 0.007797055679626856 0.16664797886217772