breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL27_S35_L001_R2_0011,998,013300,748,84099.6%150.5 bases151 bases97.9%
errorsALE-IL27_S35_L004_R1_0012,013,512303,136,61199.8%150.6 bases151 bases99.3%
errorsALE-IL27_S35_L004_R2_0012,012,100302,901,85399.7%150.5 bases151 bases98.1%
errorsALE-IL27_S35_L003_R1_0012,018,875303,923,86799.8%150.5 bases151 bases99.3%
errorsALE-IL27_S35_L002_R1_0011,986,744299,082,30799.7%150.5 bases151 bases99.4%
errorsALE-IL27_S35_L003_R2_0012,018,222303,794,90399.8%150.5 bases151 bases97.5%
errorsALE-IL27_S35_L002_R2_0011,986,471299,027,78399.6%150.5 bases151 bases97.9%
errorsALE-IL27_S35_L001_R1_0011,997,803300,726,66299.6%150.5 bases151 bases99.4%
total16,031,7402,413,342,82699.7%150.5 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652510.13.7100.0%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≤ 10000033791
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 ≤ 5000249
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.017

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.28987

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 input09:13:27 22 Apr 201609:19:42 22 Apr 20166 minutes 15 seconds
Read alignment to reference genome09:19:43 22 Apr 201609:33:19 22 Apr 201613 minutes 36 seconds
Preprocessing alignments for candidate junction identification09:33:19 22 Apr 201609:40:26 22 Apr 20167 minutes 7 seconds
Preliminary analysis of coverage distribution09:40:26 22 Apr 201609:55:49 22 Apr 201615 minutes 23 seconds
Identifying junction candidates09:55:49 22 Apr 201609:55:52 22 Apr 20163 seconds
Re-alignment to junction candidates09:55:52 22 Apr 201609:58:46 22 Apr 20162 minutes 54 seconds
Resolving alignments with junction candidates09:58:46 22 Apr 201610:25:55 22 Apr 201627 minutes 9 seconds
Creating BAM files10:25:55 22 Apr 201610:37:39 22 Apr 201611 minutes 44 seconds
Tabulating error counts10:37:39 22 Apr 201610:52:21 22 Apr 201614 minutes 42 seconds
Re-calibrating base error rates10:52:21 22 Apr 201610:52:25 22 Apr 20164 seconds
Examining read alignment evidence10:52:25 22 Apr 201612:53:41 22 Apr 20162 hours 1 minute 16 seconds
Polymorphism statistics12:53:41 22 Apr 201612:53:44 22 Apr 20163 seconds
Output12:53:44 22 Apr 201612:55:37 22 Apr 20161 minute 53 seconds
Total 3 hours 42 minutes 9 seconds