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-IL31_S39_L002_R2_0011,919,524288,934,76999.6%150.5 bases151 bases97.9%
errorsALE-IL31_S39_L001_R1_0011,927,678290,153,10399.7%150.5 bases151 bases99.4%
errorsALE-IL31_S39_L004_R2_0011,935,637291,383,02799.7%150.5 bases151 bases98.1%
errorsALE-IL31_S39_L003_R1_0011,952,993293,991,29899.8%150.5 bases151 bases99.3%
errorsALE-IL31_S39_L003_R2_0011,951,664293,760,11099.7%150.5 bases151 bases97.5%
errorsALE-IL31_S39_L002_R1_0011,920,442289,080,62199.7%150.5 bases151 bases99.4%
errorsALE-IL31_S39_L001_R2_0011,927,471290,113,89499.6%150.5 bases151 bases97.8%
errorsALE-IL31_S39_L004_R1_0011,937,371291,657,06299.8%150.5 bases151 bases99.3%
total15,472,7802,329,073,88499.7%150.5 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652493.56.8100.0%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≤ 10000013771
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 ≤ 5000333
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.023

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.29913

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 input21:47:02 20 Apr 201621:56:55 20 Apr 20169 minutes 53 seconds
Read alignment to reference genome21:56:56 20 Apr 201623:11:09 20 Apr 20161 hour 14 minutes 13 seconds
Preprocessing alignments for candidate junction identification23:11:09 20 Apr 201623:24:00 20 Apr 201612 minutes 51 seconds
Preliminary analysis of coverage distribution23:24:00 20 Apr 201623:49:06 20 Apr 201625 minutes 6 seconds
Identifying junction candidates23:49:06 20 Apr 201623:49:13 20 Apr 20167 seconds
Re-alignment to junction candidates23:49:13 20 Apr 201623:57:06 20 Apr 20167 minutes 53 seconds
Resolving alignments with junction candidates23:57:06 20 Apr 201600:46:23 21 Apr 201649 minutes 17 seconds
Creating BAM files00:46:23 21 Apr 201600:59:59 21 Apr 201613 minutes 36 seconds
Tabulating error counts00:59:59 21 Apr 201601:23:25 21 Apr 201623 minutes 26 seconds
Re-calibrating base error rates01:23:25 21 Apr 201601:23:29 21 Apr 20164 seconds
Examining read alignment evidence01:23:29 21 Apr 201603:52:06 21 Apr 20162 hours 28 minutes 37 seconds
Polymorphism statistics03:52:06 21 Apr 201603:52:09 21 Apr 20163 seconds
Output03:52:09 21 Apr 201603:55:02 21 Apr 20162 minutes 53 seconds
Total 6 hours 7 minutes 59 seconds