breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR3480975_pass_R1.good.fq1,095,538273,273,523100.0%249.4 bases250 bases99.3%
errorsSRR3480975_pass_R2.good.fq1,095,538273,273,523100.0%249.4 bases250 bases95.7%
total2,191,076546,547,046100.0%249.4 bases250 bases97.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0077794,646,332117.22.4100.0%Escherichia coli str. K-12 substr. W3110, complete sequence.
total4,646,332100.0%

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.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 10000020715
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500079
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.009

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0077790.80219

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.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input23:27:44 14 Feb 202023:28:16 14 Feb 202032 seconds
Read alignment to reference genome23:28:16 14 Feb 202023:35:36 14 Feb 20207 minutes 20 seconds
Preprocessing alignments for candidate junction identification23:35:36 14 Feb 202023:36:10 14 Feb 202034 seconds
Preliminary analysis of coverage distribution23:36:10 14 Feb 202023:37:55 14 Feb 20201 minute 45 seconds
Identifying junction candidates23:37:55 14 Feb 202023:37:57 14 Feb 20202 seconds
Re-alignment to junction candidates23:37:57 14 Feb 202023:39:38 14 Feb 20201 minute 41 seconds
Resolving best read alignments23:39:38 14 Feb 202023:40:38 14 Feb 20201 minute 0 seconds
Creating BAM files23:40:38 14 Feb 202023:42:14 14 Feb 20201 minute 36 seconds
Tabulating error counts23:42:14 14 Feb 202023:42:54 14 Feb 202040 seconds
Re-calibrating base error rates23:42:54 14 Feb 202023:42:54 14 Feb 20200 seconds
Examining read alignment evidence23:42:54 14 Feb 202023:50:37 14 Feb 20207 minutes 43 seconds
Polymorphism statistics23:50:37 14 Feb 202023:50:37 14 Feb 20200 seconds
Output23:50:37 14 Feb 202023:51:04 14 Feb 202027 seconds
Total 23 minutes 20 seconds