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-IL32_S40_L002_R2_0011,714,162258,024,78299.7%150.5 bases151 bases98.2%
errorsALE-IL32_S40_L003_R1_0011,744,748262,645,56099.9%150.5 bases151 bases99.5%
errorsALE-IL32_S40_L003_R2_0011,742,511262,279,01299.8%150.5 bases151 bases97.9%
errorsALE-IL32_S40_L001_R2_0011,727,231259,972,08999.7%150.5 bases151 bases98.2%
errorsALE-IL32_S40_L004_R1_0011,733,176260,914,93299.9%150.5 bases151 bases99.5%
errorsALE-IL32_S40_L004_R2_0011,730,354260,470,05599.7%150.5 bases151 bases98.4%
errorsALE-IL32_S40_L001_R1_0011,730,043260,408,96399.8%150.5 bases151 bases99.6%
errorsALE-IL32_S40_L002_R1_0011,717,172258,488,48499.8%150.5 bases151 bases99.6%
total13,839,3972,083,203,87799.8%150.5 bases151 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652442.56.3100.0%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≤ 1000009938
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 ≤ 5000211
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.014

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.32846

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 input12:07:41 21 Apr 201612:12:59 21 Apr 20165 minutes 18 seconds
Read alignment to reference genome12:12:59 21 Apr 201612:27:32 21 Apr 201614 minutes 33 seconds
Preprocessing alignments for candidate junction identification12:27:32 21 Apr 201612:34:00 21 Apr 20166 minutes 28 seconds
Preliminary analysis of coverage distribution12:34:00 21 Apr 201612:49:34 21 Apr 201615 minutes 34 seconds
Identifying junction candidates12:49:34 21 Apr 201612:49:36 21 Apr 20162 seconds
Re-alignment to junction candidates12:49:36 21 Apr 201612:53:01 21 Apr 20163 minutes 25 seconds
Resolving alignments with junction candidates12:53:01 21 Apr 201613:20:51 21 Apr 201627 minutes 50 seconds
Creating BAM files13:20:51 21 Apr 201613:40:26 21 Apr 201619 minutes 35 seconds
Tabulating error counts13:40:26 21 Apr 201613:56:14 21 Apr 201615 minutes 48 seconds
Re-calibrating base error rates13:56:15 21 Apr 201613:56:20 21 Apr 20165 seconds
Examining read alignment evidence13:56:20 21 Apr 201615:53:07 21 Apr 20161 hour 56 minutes 47 seconds
Polymorphism statistics15:53:07 21 Apr 201615:53:10 21 Apr 20163 seconds
Output15:53:10 21 Apr 201615:55:26 21 Apr 20162 minutes 16 seconds
Total 3 hours 47 minutes 44 seconds