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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsGlucose_ALE_4_FLASK_403_Isolate_1_S3_L001_R1_001.good.fq734,919110,056,417100.0%149.8 bases239 bases98.6%
errorsGlucose_ALE_4_FLASK_403_Isolate_1_S3_L001_R2_001.good.fq734,919110,218,047100.0%150.0 bases239 bases94.2%
total1,469,838220,274,464100.0%149.9 bases239 bases96.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65246.33.0100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 10000019752
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 threshold100 ≤ n ≤ 500066
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.88379

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 input10:04:05 22 May 201910:04:22 22 May 201917 seconds
Read alignment to reference genome10:04:23 22 May 201910:08:12 22 May 20193 minutes 49 seconds
Preprocessing alignments for candidate junction identification10:08:12 22 May 201910:08:31 22 May 201919 seconds
Preliminary analysis of coverage distribution10:08:31 22 May 201910:09:22 22 May 201951 seconds
Identifying junction candidates10:09:22 22 May 201910:11:05 22 May 20191 minute 43 seconds
Re-alignment to junction candidates10:11:05 22 May 201910:12:08 22 May 20191 minute 3 seconds
Resolving best read alignments10:12:08 22 May 201910:12:40 22 May 201932 seconds
Creating BAM files10:12:40 22 May 201910:13:26 22 May 201946 seconds
Tabulating error counts10:13:26 22 May 201910:13:44 22 May 201918 seconds
Re-calibrating base error rates10:13:44 22 May 201910:13:44 22 May 20190 seconds
Examining read alignment evidence10:13:44 22 May 201910:16:57 22 May 20193 minutes 13 seconds
Polymorphism statistics10:16:57 22 May 201910:16:57 22 May 20190 seconds
Output10:16:57 22 May 201910:17:07 22 May 201910 seconds
Total 13 minutes 1 second