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_3_FLASK_72_Isolate_1_S2_L001_R1_001.good.fq3,629,112680,131,332100.0%187.4 bases239 bases99.4%
errorsGlucose_ALE_3_FLASK_72_Isolate_1_S2_L001_R2_001.good.fq3,629,112679,572,919100.0%187.3 bases239 bases93.2%
total7,258,2241,359,704,251100.0%187.3 bases239 bases96.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652292.713.7100.0%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≤ 10000023971
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 ≤ 500072
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.008

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.66256

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 input21:00:53 22 May 201921:02:32 22 May 20191 minute 39 seconds
Read alignment to reference genome21:02:32 22 May 201921:26:30 22 May 201923 minutes 58 seconds
Preprocessing alignments for candidate junction identification21:26:30 22 May 201921:28:13 22 May 20191 minute 43 seconds
Preliminary analysis of coverage distribution21:28:13 22 May 201921:33:51 22 May 20195 minutes 38 seconds
Identifying junction candidates21:33:51 22 May 201921:35:12 22 May 20191 minute 21 seconds
Re-alignment to junction candidates21:35:12 22 May 201921:41:44 22 May 20196 minutes 32 seconds
Resolving best read alignments21:41:44 22 May 201921:44:42 22 May 20192 minutes 58 seconds
Creating BAM files21:44:42 22 May 201921:49:41 22 May 20194 minutes 59 seconds
Tabulating error counts21:49:41 22 May 201921:51:37 22 May 20191 minute 56 seconds
Re-calibrating base error rates21:51:37 22 May 201921:51:38 22 May 20191 second
Examining read alignment evidence21:51:38 22 May 201922:12:04 22 May 201920 minutes 26 seconds
Polymorphism statistics22:12:04 22 May 201922:12:05 22 May 20191 second
Output22:12:05 22 May 201922:12:36 22 May 201931 seconds
Total 1 hour 11 minutes 43 seconds