BRESEQ :: Summary Statistics

breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

	read file	reads	bases	passed filters	average	longest	mapped
errors	Evo04sdhCadhBEvo02EP_S21_L001_R2_001.good.fq	508,439	133,274,722	100.0%	262.1 bases	289 bases	97.8%
errors	Evo04sdhCadhBEvo02EP_S21_L001_R1_001.good.fq	508,439	133,225,159	100.0%	262.0 bases	289 bases	98.9%
	total	1,016,878	266,499,881	100.0%	262.1 bases	289 bases	98.3%

		seq id	length	fit mean	fit dispersion	% mapped reads	description
coverage	distribution	NC_000913	4,641,653	59.5	5.0	100.0%	Escherichia coli str. K-12 sbstr. MG1655, complete genome. Live strain from Systems Biology Research Group
		total	4,641,653			100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

option	limit	actual
Number of alignment pairs examined for constructing junction candidates	≤ 100000	12035
Coverage evenness (position-hash) score of junction candidates	≥ 2	≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold	100 ≤ n ≤ 5000	58
Total length of all junction candidates (factor times the reference genome length)	≤ 0.1	0.007

reference sequence	pr(no read start)
NC_000913	0.91629

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

option	value
Coverage evenness (position-hash) score of predicted junctions must be	≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be	≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction	≥ 6

option	value
Mode	Full Polymorphism
Ploidy	1 (haploid)
Consensus mutation E-value cutoff	10
Consensus frequency cutoff	OFF
Consensus minimum variant coverage each strand	OFF
Consensus minimum total coverage each strand	OFF
Consensus minimum variant coverage	OFF
Consensus minimum total coverage	OFF
Polymorphism E-value cutoff	2
Polymorphism frequency cutoff	0.025
Polymorphism minimum variant coverage each strand	2
Polymorphism minimum total coverage each strand	OFF
Polymorphism minimum variant coverage	OFF
Polymorphism minimum total coverage	OFF
Polymorphism bias cutoff	OFF
Predict indel polymorphisms	YES
Skip indel polymorphisms in homopolymers runs of	≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by	≥5 bases

program	version
bowtie2	2.2.8
R	3.3.1

step	start	end	elapsed
Read and reference sequence file input	08:51:20 18 Mar 2018	08:51:36 18 Mar 2018	16 seconds
Read alignment to reference genome	08:51:36 18 Mar 2018	08:52:46 18 Mar 2018	1 minute 10 seconds
Preprocessing alignments for candidate junction identification	08:52:46 18 Mar 2018	08:53:04 18 Mar 2018	18 seconds
Preliminary analysis of coverage distribution	08:53:04 18 Mar 2018	08:53:42 18 Mar 2018	38 seconds
Identifying junction candidates	08:53:42 18 Mar 2018	08:54:19 18 Mar 2018	37 seconds
Re-alignment to junction candidates	08:54:19 18 Mar 2018	08:54:31 18 Mar 2018	12 seconds
Resolving best read alignments	08:54:31 18 Mar 2018	08:55:02 18 Mar 2018	31 seconds
Creating BAM files	08:55:02 18 Mar 2018	08:55:31 18 Mar 2018	29 seconds
Tabulating error counts	08:55:31 18 Mar 2018	08:55:53 18 Mar 2018	22 seconds
Re-calibrating base error rates	08:55:53 18 Mar 2018	08:55:53 18 Mar 2018	0 seconds
Examining read alignment evidence	08:55:53 18 Mar 2018	09:08:45 18 Mar 2018	12 minutes 52 seconds
Polymorphism statistics	09:08:45 18 Mar 2018	09:08:46 18 Mar 2018	1 second
Output	09:08:46 18 Mar 2018	09:09:01 18 Mar 2018	15 seconds
Total			17 minutes 41 seconds