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_66_Isolate_1_S3_L001_R1_001.good.fq2,763,238494,089,277100.0%178.8 bases239 bases99.6%
errorsGlucose_ALE_4_FLASK_66_Isolate_1_S3_L001_R2_001.good.fq2,763,238493,934,520100.0%178.8 bases239 bases94.3%
total5,526,476988,023,797100.0%178.8 bases239 bases96.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652211.510.3100.0%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≤ 10000015862
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 ≤ 500041
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.004

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.70866

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 input13:03:11 23 May 201913:04:18 23 May 20191 minute 7 seconds
Read alignment to reference genome13:04:18 23 May 201913:21:19 23 May 201917 minutes 1 second
Preprocessing alignments for candidate junction identification13:21:19 23 May 201913:22:36 23 May 20191 minute 17 seconds
Preliminary analysis of coverage distribution13:22:36 23 May 201913:26:47 23 May 20194 minutes 11 seconds
Identifying junction candidates13:26:47 23 May 201913:27:16 23 May 201929 seconds
Re-alignment to junction candidates13:27:16 23 May 201913:31:52 23 May 20194 minutes 36 seconds
Resolving best read alignments13:31:52 23 May 201913:34:03 23 May 20192 minutes 11 seconds
Creating BAM files13:34:03 23 May 201913:37:46 23 May 20193 minutes 43 seconds
Tabulating error counts13:37:46 23 May 201913:39:09 23 May 20191 minute 23 seconds
Re-calibrating base error rates13:39:09 23 May 201913:39:10 23 May 20191 second
Examining read alignment evidence13:39:10 23 May 201913:53:59 23 May 201914 minutes 49 seconds
Polymorphism statistics13:53:59 23 May 201913:53:59 23 May 20190 seconds
Output13:53:59 23 May 201913:54:23 23 May 201924 seconds
Total 51 minutes 12 seconds