BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3081736.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 = 2,642,489
number of mapped reads = 2,413,751 (91.34%)
number of supplementary alignments = 16,988 (0.64%)
number of secondary alignments = 0
number of mapped bases = 163,082,523 bp
number of sequenced bases = 163,024,423 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 90,784
duplication rate = 3%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.4502
>>>>>>> ACTG content
number of A's = 44,972,217 bp (27.59%)
number of C's = 31,431,165 bp (19.28%)
number of T's = 49,879,507 bp (30.6%)
number of G's = 36,739,653 bp (22.54%)
number of N's = 1,881 bp (0%)
GC percentage = 41.82%
>>>>>>> Mismatches and indels
general error rate = 0.008
number of mismatches = 1,278,210
number of insertions = 11,583
mapped reads with insertion percentage = 0.47%
number of deletions = 32,486
mapped reads with deletion percentage = 1.33%
homopolymer indels = 46.47%
>>>>>>> Coverage
mean coverageData = 0.0527X
std coverageData = 0.3737X
There is a 4.45% of reference with a coverageData >= 1X
There is a 0.61% of reference with a coverageData >= 2X
There is a 0.1% 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 12970435 0.05203772391002388 0.5823876667181692
chr2 243199373 14084666 0.057914072007085315 0.47310594870975947
chr3 198022430 10938110 0.055236722425838325 0.2710636041820702
chr4 191154276 10735928 0.056163682155872884 0.29989557577793313
chr5 180915260 10013938 0.05535153861537164 0.268857922377919
chr6 171115067 9398149 0.05492297764754988 0.29393547259456265
chr7 159138663 9086217 0.057096225572788685 0.4483107310530486
chr8 146364022 8167667 0.05580378899399198 0.4121589349191444
chr9 141213431 6807654 0.04820826143654848 0.3604769129214898
chr10 135534747 7712866 0.05690692734314102 0.4373224473393596
chr11 135006516 7590858 0.05622586394274481 0.338334780042213
chr12 133851895 7319940 0.05468686117592881 0.2693169592479383
chr13 115169878 5225027 0.04536799978202634 0.243006897541365
chr14 107349540 5060164 0.047137267658529325 0.2612964119453574
chr15 102531392 4611037 0.04497195356520665 0.24732933418623904
chr16 90354753 4662022 0.05159686508135328 0.30243912661590083
chr17 81195210 4256209 0.052419459226720394 0.28875532179845875
chr18 78077248 4311122 0.05521611110063716 0.620671734666024
chr19 59128983 3141758 0.05313397661515673 0.4955102914632751
chr20 63025520 3178645 0.050434252664634895 0.2683625853315475
chr21 48129895 2108164 0.04380154995143871 0.2636233008590825
chr22 51304566 1733733 0.033792957141475476 0.21053662206051096
chrMT 16571 29655 1.7895721441071752 1.6624278089700233
chrX 155270560 9520385 0.06131481074068387 0.31233361623036776
chrY 59373566 418174 0.007043100628316649 0.17777690097997245