BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3081945.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,006,851
number of mapped reads = 2,773,598 (92.24%)
number of supplementary alignments = 17,164 (0.57%)
number of secondary alignments = 0
number of mapped bases = 189,061,575 bp
number of sequenced bases = 188,989,871 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 129,979
duplication rate = 3.86%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.6918
>>>>>>> ACTG content
number of A's = 53,451,969 bp (28.28%)
number of C's = 35,044,032 bp (18.54%)
number of T's = 59,608,951 bp (31.54%)
number of G's = 40,860,500 bp (21.62%)
number of N's = 24,419 bp (0.01%)
GC percentage = 40.16%
>>>>>>> Mismatches and indels
general error rate = 0.0076
number of mismatches = 1,413,013
number of insertions = 12,995
mapped reads with insertion percentage = 0.46%
number of deletions = 40,422
mapped reads with deletion percentage = 1.44%
homopolymer indels = 49.03%
>>>>>>> Coverage
mean coverageData = 0.0611X
std coverageData = 0.4344X
There is a 5.13% of reference with a coverageData >= 1X
There is a 0.73% of reference with a coverageData >= 2X
There is a 0.12% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% 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 17403325 0.06982259434370677 0.6754694832654936
chr2 243199373 16335608 0.06716961396113467 0.5440090522405739
chr3 198022430 12664429 0.06395451767761864 0.29092170756280816
chr4 191154276 9189184 0.04807208184032462 0.26468038176834574
chr5 180915260 9751474 0.05390078205674856 0.26507903487905515
chr6 171115067 16434665 0.09604452306937998 0.4462983869050382
chr7 159138663 12123213 0.07618018633221771 0.6062414128538307
chr8 146364022 9870117 0.06743540430994716 0.6736590536234629
chr9 141213431 8845529 0.06263943123087208 0.44403788785047965
chr10 135534747 7910235 0.05836315170160756 0.43873760637866105
chr11 135006516 8645915 0.06404072378254691 0.3348427016427419
chr12 133851895 7925832 0.05921344632438712 0.28486246031193146
chr13 115169878 5496749 0.04772731460217402 0.2485784773034244
chr14 107349540 4645996 0.0432791421369854 0.25517781130037537
chr15 102531392 4430762 0.04321371156260124 0.23776050686510103
chr16 90354753 4405053 0.0487528641686398 0.2926011593722864
chr17 81195210 5699692 0.07019739218606615 0.345959234330089
chr18 78077248 5162465 0.06611996621602237 0.6485935599141411
chr19 59128983 3784647 0.06400663106280723 0.549946174590078
chr20 63025520 5114288 0.08114630390990824 0.33163374763562453
chr21 48129895 1956709 0.04065475314251153 0.25334900899466156
chr22 51304566 1672939 0.03260799438396964 0.20376636954024868
chrMT 16571 44711 2.698147365880152 2.252646002437593
chrX 155270560 9174533 0.05908739557582584 0.3036826227689732
chrY 59373566 373505 0.006290762458161937 0.144240228287606