BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3082982.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 = 3,284,571
number of mapped reads = 2,389,887 (72.76%)
number of supplementary alignments = 20,676 (0.63%)
number of secondary alignments = 0
number of mapped bases = 161,121,100 bp
number of sequenced bases = 161,050,592 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 95,938
duplication rate = 2.65%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9587
>>>>>>> ACTG content
number of A's = 45,418,067 bp (28.2%)
number of C's = 29,448,832 bp (18.29%)
number of T's = 51,047,876 bp (31.7%)
number of G's = 35,120,506 bp (21.81%)
number of N's = 15,311 bp (0.01%)
GC percentage = 40.09%
>>>>>>> Mismatches and indels
general error rate = 0.0105
number of mismatches = 1,660,548
number of insertions = 15,513
mapped reads with insertion percentage = 0.64%
number of deletions = 40,578
mapped reads with deletion percentage = 1.68%
homopolymer indels = 47.37%
>>>>>>> Coverage
mean coverageData = 0.052X
std coverageData = 0.5097X
There is a 4.45% of reference with a coverageData >= 1X
There is a 0.51% of reference with a coverageData >= 2X
There is a 0.09% of reference with a coverageData >= 3X
There is a 0.02% 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 14895660 0.059761776882393404 0.8117555960751095
chr2 243199373 16534816 0.0679887279150181 0.7057860448090606
chr3 198022430 10964178 0.05536836407875613 0.2657813453506796
chr4 191154276 11086921 0.0579998587109817 0.2835818398725286
chr5 180915260 8094404 0.04474141097881958 0.2428566720579928
chr6 171115067 11394105 0.06658738590214268 0.4877655765139893
chr7 159138663 9559830 0.06007232824370279 0.6619453277736236
chr8 146364022 13472950 0.09205096864583293 0.5949537604802477
chr9 141213431 5070511 0.03590671909954514 0.5089055870604086
chr10 135534747 6240070 0.04604037073976314 0.3810266273339893
chr11 135006516 5608672 0.041543713341954544 0.40510140641949643
chr12 133851895 5272118 0.03938769787308577 0.24282658311699834
chr13 115169878 3946455 0.03426638170095136 0.20563628186289729
chr14 107349540 3562015 0.03318146496016657 0.3153021018407137
chr15 102531392 3057230 0.029817502136321332 0.19355279910910758
chr16 90354753 4107950 0.04546468075675001 0.3483049210486786
chr17 81195210 4071083 0.050139447881223535 0.3435288946621971
chr18 78077248 5506157 0.07052191439944194 1.3273816720793794
chr19 59128983 2621334 0.04433247228351619 0.569503798965042
chr20 63025520 2900221 0.04601661358763878 0.2896903039308618
chr21 48129895 3865507 0.08031405428995846 0.34255516638811867
chr22 51304566 2075674 0.04045788049352177 0.22495672535417177
chrMT 16571 50874 3.0700621567799167 3.192453086626487
chrX 155270560 6840965 0.0440583520791063 0.33983367978836443
chrY 59373566 321400 0.005413183368504429 0.1218015182890914