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-IL8_S8_L002_R2_0011,571,222236,538,39999.6%150.5 bases151 bases97.5%
errorsALE-IL8_S8_L003_R2_0011,592,780239,774,83499.7%150.5 bases151 bases97.1%
errorsALE-IL8_S8_L001_R2_0011,578,250237,584,96799.5%150.5 bases151 bases97.5%
errorsALE-IL8_S8_L004_R2_0011,600,303240,929,27599.6%150.6 bases151 bases97.7%
errorsALE-IL8_S8_L003_R1_0011,597,124240,457,83899.9%150.6 bases151 bases99.5%
errorsALE-IL8_S8_L001_R1_0011,583,311238,358,10299.9%150.5 bases151 bases99.6%
errorsALE-IL8_S8_L004_R1_0011,605,547241,740,85099.9%150.6 bases151 bases99.5%
errorsALE-IL8_S8_L002_R1_0011,576,357237,324,20599.9%150.6 bases151 bases99.6%
total12,704,8941,912,708,47099.7%150.5 bases151 bases98.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652403.84.2100.0%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≤ 1000006131
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 ≤ 5000194
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.013

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.35608

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 input14:44:23 21 Apr 201614:49:47 21 Apr 20165 minutes 24 seconds
Read alignment to reference genome14:49:47 21 Apr 201615:03:14 21 Apr 201613 minutes 27 seconds
Preprocessing alignments for candidate junction identification15:03:14 21 Apr 201615:08:57 21 Apr 20165 minutes 43 seconds
Preliminary analysis of coverage distribution15:08:57 21 Apr 201615:23:00 21 Apr 201614 minutes 3 seconds
Identifying junction candidates15:23:00 21 Apr 201615:23:01 21 Apr 20161 second
Re-alignment to junction candidates15:23:01 21 Apr 201615:25:45 21 Apr 20162 minutes 44 seconds
Resolving alignments with junction candidates15:25:45 21 Apr 201615:39:56 21 Apr 201614 minutes 11 seconds
Creating BAM files15:39:56 21 Apr 201615:50:21 21 Apr 201610 minutes 25 seconds
Tabulating error counts15:50:21 21 Apr 201616:03:48 21 Apr 201613 minutes 27 seconds
Re-calibrating base error rates16:03:48 21 Apr 201616:03:55 21 Apr 20167 seconds
Examining read alignment evidence16:03:55 21 Apr 201618:03:13 21 Apr 20161 hour 59 minutes 18 seconds
Polymorphism statistics18:03:13 21 Apr 201618:03:16 21 Apr 20163 seconds
Output18:03:16 21 Apr 201618:05:31 21 Apr 20162 minutes 15 seconds
Total 3 hours 21 minutes 8 seconds