breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR4302518_R1.good.fq14,433,8991,385,175,051100.0%96.0 bases96 bases97.4%
errorsSRR4302518_R2.good.fq14,433,8991,385,175,051100.0%96.0 bases96 bases98.1%
total28,867,7982,770,350,102100.0%96.0 bases96 bases97.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,639,221579.69.3100.0%Escherichia coli K12, complete genome.
total4,639,221100.0%

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≤ 10000030503
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 ≤ 5000996
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.043

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.08348

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input10:28:00 17 Jan 202310:35:45 17 Jan 20237 minutes 45 seconds
Read alignment to reference genome10:35:46 17 Jan 202311:16:10 17 Jan 202340 minutes 24 seconds
Preprocessing alignments for candidate junction identification11:16:10 17 Jan 202311:22:49 17 Jan 20236 minutes 39 seconds
Preliminary analysis of coverage distribution11:22:49 17 Jan 202311:36:22 17 Jan 202313 minutes 33 seconds
Identifying junction candidates11:36:22 17 Jan 202311:36:29 17 Jan 20237 seconds
Re-alignment to junction candidates11:36:29 17 Jan 202311:48:04 17 Jan 202311 minutes 35 seconds
Resolving best read alignments11:48:04 17 Jan 202311:56:43 17 Jan 20238 minutes 39 seconds
Creating BAM files11:56:43 17 Jan 202312:08:51 17 Jan 202312 minutes 8 seconds
Tabulating error counts12:08:51 17 Jan 202312:12:48 17 Jan 20233 minutes 57 seconds
Re-calibrating base error rates12:12:48 17 Jan 202312:12:49 17 Jan 20231 second
Examining read alignment evidence12:12:49 17 Jan 202312:59:15 17 Jan 202346 minutes 26 seconds
Polymorphism statistics12:59:15 17 Jan 202312:59:16 17 Jan 20231 second
Output12:59:16 17 Jan 202313:00:53 17 Jan 20231 minute 37 seconds
Total 2 hours 32 minutes 52 seconds