BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714067.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 621,540
number of mapped reads = 37,789 (6.08%)
number of supplementary alignments = 864 (0.14%)
number of secondary alignments = 0
number of mapped bases = 3,149,707 bp
number of sequenced bases = 3,123,678 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 34,074
duplication rate = 32.15%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 27.61
>>>>>>> ACTG content
number of A's = 370,465 bp (11.86%)
number of C's = 241,269 bp (7.72%)
number of T's = 297,424 bp (9.52%)
number of G's = 2,214,436 bp (70.89%)
number of N's = 84 bp (0%)
GC percentage = 78.62%
>>>>>>> Mismatches and indels
general error rate = 0.0312
number of mismatches = 81,216
number of insertions = 3,163
mapped reads with insertion percentage = 6.33%
number of deletions = 4,344
mapped reads with deletion percentage = 11.07%
homopolymer indels = 40.87%
>>>>>>> Coverage
mean coverageData = 0.001X
std coverageData = 2.2946X
There is a 0.01% of reference with a coverageData >= 1X
There is a 0% of reference with a coverageData >= 2X
There is a 0% of reference with a coverageData >= 3X
There is a 0% 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 40187 1.6123129338161207E-4 0.07320767478539333
chr2 243199373 2076230 0.008537151944055382 8.171098598063486
chr3 198022430 55119 2.783472559143931E-4 0.12089848140326827
chr4 191154276 85189 4.4565573830009433E-4 0.1690917273446323
chr5 180915260 29447 1.6276681137898484E-4 0.04604489295957982
chr6 171115067 25139 1.469128373131514E-4 0.054865758911345645
chr7 159138663 49040 3.0815892929802986E-4 0.2708274222312063
chr8 146364022 76045 5.195607428716328E-4 0.212298950720362
chr9 141213431 11571 8.193979792191297E-5 0.021281699765569748
chr10 135534747 44720 3.2995228891377946E-4 0.10683107690699584
chr11 135006516 32230 2.3872921807714822E-4 0.10030907155231744
chr12 133851895 60773 4.540316743367735E-4 0.15306382557211884
chr13 115169878 10417 9.044899743663878E-5 0.0327447211134901
chr14 107349540 40295 3.753625772406663E-4 0.15318516428980697
chr15 102531392 18193 1.7743834005491704E-4 0.06385325137952826
chr16 90354753 17707 1.9597198168423967E-4 0.07187935583086001
chr17 81195210 20740 2.5543378728868363E-4 0.11898081819667959
chr18 78077248 15558 1.9926419537737806E-4 0.07344745259579143
chr19 59128983 36708 6.208123011349611E-4 0.2532056624485594
chr20 63025520 13242 2.101053668418761E-4 0.06042036315878554
chr21 48129895 3215 6.679840045360582E-5 0.012200967016172749
chr22 51304566 3294 6.420481171208036E-5 0.013477989176962003
chrMT 16571 2323 0.1401846599481021 1.0347971971764718
chrX 155270560 377610 0.0024319484646670945 0.34017364707333314
chrY 59373566 4715 7.941244425170623E-5 0.02473148623927422