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-IL24_S32_L002_R1_0011,484,238223,460,60199.9%150.6 bases151 bases99.6%
errorsALE-IL24_S32_L003_R2_0011,504,467226,483,94399.8%150.5 bases151 bases97.8%
errorsALE-IL24_S32_L001_R1_0011,493,550224,848,71699.9%150.5 bases151 bases99.6%
errorsALE-IL24_S32_L002_R2_0011,480,771222,925,72999.7%150.5 bases151 bases98.1%
errorsALE-IL24_S32_L003_R1_0011,507,167226,920,11899.9%150.6 bases151 bases99.6%
errorsALE-IL24_S32_L001_R2_0011,490,204224,331,71799.7%150.5 bases151 bases98.0%
errorsALE-IL24_S32_L004_R1_0011,513,288227,854,52199.9%150.6 bases151 bases99.6%
errorsALE-IL24_S32_L004_R2_0011,510,053227,345,29499.7%150.6 bases151 bases98.3%
total11,983,7381,804,170,63999.8%150.6 bases151 bases98.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652382.75.7100.0%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≤ 1000009034
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 ≤ 5000176
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.37014

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 input22:49:20 21 Apr 201622:53:43 21 Apr 20164 minutes 23 seconds
Read alignment to reference genome22:53:44 21 Apr 201623:04:10 21 Apr 201610 minutes 26 seconds
Preprocessing alignments for candidate junction identification23:04:10 21 Apr 201623:09:05 21 Apr 20164 minutes 55 seconds
Preliminary analysis of coverage distribution23:09:05 21 Apr 201623:21:51 21 Apr 201612 minutes 46 seconds
Identifying junction candidates23:21:51 21 Apr 201623:21:52 21 Apr 20161 second
Re-alignment to junction candidates23:21:52 21 Apr 201623:23:54 21 Apr 20162 minutes 2 seconds
Resolving alignments with junction candidates23:23:54 21 Apr 201623:37:12 21 Apr 201613 minutes 18 seconds
Creating BAM files23:37:12 21 Apr 201623:44:48 21 Apr 20167 minutes 36 seconds
Tabulating error counts23:44:48 21 Apr 201623:59:25 21 Apr 201614 minutes 37 seconds
Re-calibrating base error rates23:59:25 21 Apr 201623:59:28 21 Apr 20163 seconds
Examining read alignment evidence23:59:28 21 Apr 201601:44:09 22 Apr 20161 hour 44 minutes 41 seconds
Polymorphism statistics01:44:09 22 Apr 201601:44:13 22 Apr 20164 seconds
Output01:44:13 22 Apr 201601:46:31 22 Apr 20162 minutes 18 seconds
Total 2 hours 57 minutes 10 seconds