BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3081059.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 = 2,758,463
number of mapped reads = 2,506,883 (90.88%)
number of supplementary alignments = 29,769 (1.08%)
number of secondary alignments = 0
number of mapped bases = 168,714,001 bp
number of sequenced bases = 168,653,326 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 122,284
duplication rate = 3.81%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.8383
>>>>>>> ACTG content
number of A's = 47,507,549 bp (28.17%)
number of C's = 31,942,023 bp (18.94%)
number of T's = 52,555,199 bp (31.16%)
number of G's = 36,646,633 bp (21.73%)
number of N's = 1,922 bp (0%)
GC percentage = 40.67%
>>>>>>> Mismatches and indels
general error rate = 0.0092
number of mismatches = 1,530,002
number of insertions = 13,500
mapped reads with insertion percentage = 0.53%
number of deletions = 37,082
mapped reads with deletion percentage = 1.46%
homopolymer indels = 46.63%
>>>>>>> Coverage
mean coverageData = 0.0545X
std coverageData = 0.4466X
There is a 4.48% of reference with a coverageData >= 1X
There is a 0.69% of reference with a coverageData >= 2X
There is a 0.13% 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 0.01% 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 14789275 0.05933495748441887 0.7608489312364658
chr2 243199373 11629187 0.04781750403608154 0.4587299622793112
chr3 198022430 13909672 0.07024291137120174 0.31189907191690563
chr4 191154276 9786670 0.0511977560993718 0.2998609114995501
chr5 180915260 9605163 0.05309205536337841 0.26824147238450075
chr6 171115067 15353383 0.0897254886385896 0.6236963469928858
chr7 159138663 8032866 0.050477148975419 0.347877796772993
chr8 146364022 11980853 0.08185654395313077 0.535334118546663
chr9 141213431 8432980 0.05971797399356439 0.5060703869339779
chr10 135534747 7726378 0.05700662133526541 0.45099345965344234
chr11 135006516 6978707 0.05169163094320573 0.35699758054455766
chr12 133851895 8466988 0.06325639244778716 0.30585486955104624
chr13 115169878 4088235 0.03549743275754794 0.21983016222577906
chr14 107349540 5192368 0.048368795991114634 0.3334242363881564
chr15 102531392 3891873 0.03795786757679053 0.22807170484511372
chr16 90354753 3865755 0.04278419088810967 0.33532595761240147
chr17 81195210 3554106 0.04377236046313569 0.2581066627145406
chr18 78077248 4268591 0.05467138134786718 0.9235640486871528
chr19 59128983 3302314 0.05584932857715479 0.5506217769895809
chr20 63025520 2813324 0.044637854634122814 0.2766330377477957
chr21 48129895 3938276 0.08182598362202952 0.3935726133431388
chr22 51304566 1537789 0.029973725925290937 0.19949716982265137
chrMT 16571 88776 5.3573109649387485 3.6080114454574517
chrX 155270560 4995868 0.03217524300807571 0.2492210600787713
chrY 59373566 484604 0.00816194870289583 0.21674826172127648