breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-BUT4-7_S9_L001_R2_0011,029,164154,816,230100.0%150.4 bases151 bases99.0%
errorsqtrim-BUT4-7_S9_L001_R1_0011,029,289154,915,889100.0%150.5 bases151 bases99.7%
total2,058,453309,732,119100.0%150.5 bases151 bases99.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65266.31.298.3%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≤ 1000001545
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 ≤ 500031
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81015

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 cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
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

Execution Times

stepstartendelapsed
Read and reference sequence file input15:09:43 02 Jan 201715:10:35 02 Jan 201752 seconds
Read alignment to reference genome15:10:36 02 Jan 201715:16:27 02 Jan 20175 minutes 51 seconds
Preprocessing alignments for candidate junction identification15:16:27 02 Jan 201715:17:36 02 Jan 20171 minute 9 seconds
Preliminary analysis of coverage distribution15:17:36 02 Jan 201715:19:20 02 Jan 20171 minute 44 seconds
Identifying junction candidates15:19:20 02 Jan 201715:19:21 02 Jan 20171 second
Re-alignment to junction candidates15:19:21 02 Jan 201715:20:28 02 Jan 20171 minute 7 seconds
Resolving alignments with junction candidates15:20:28 02 Jan 201715:22:25 02 Jan 20171 minute 57 seconds
Creating BAM files15:22:25 02 Jan 201715:23:47 02 Jan 20171 minute 22 seconds
Tabulating error counts15:23:47 02 Jan 201715:25:20 02 Jan 20171 minute 33 seconds
Re-calibrating base error rates15:25:20 02 Jan 201715:25:21 02 Jan 20171 second
Examining read alignment evidence15:25:21 02 Jan 201715:38:05 02 Jan 201712 minutes 44 seconds
Polymorphism statistics15:38:05 02 Jan 201715:38:06 02 Jan 20171 second
Output15:38:06 02 Jan 201715:38:24 02 Jan 201718 seconds
Total 28 minutes 40 seconds