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-IL1_S1_L002_R2_0011,671,017251,531,99499.6%150.5 bases151 bases96.6%
errorsALE-IL1_S1_L004_R2_0011,707,100256,976,17399.6%150.5 bases151 bases96.9%
errorsALE-IL1_S1_L004_R1_0011,709,362257,339,74099.8%150.5 bases151 bases99.2%
errorsALE-IL1_S1_L003_R1_0011,693,880254,991,52599.7%150.5 bases151 bases99.0%
errorsALE-IL1_S1_L001_R1_0011,673,482251,896,81999.5%150.5 bases151 bases99.2%
errorsALE-IL1_S1_L003_R2_0011,692,788254,800,63099.7%150.5 bases151 bases96.2%
errorsALE-IL1_S1_L002_R1_0011,669,970251,385,55499.5%150.5 bases151 bases99.2%
errorsALE-IL1_S1_L001_R2_0011,674,658252,065,20899.6%150.5 bases151 bases96.5%
total13,492,2572,030,987,64399.6%150.5 bases151 bases97.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652425.63.1100.0%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≤ 1000009250
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 ≤ 5000250
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_0009130.33945

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 input06:55:01 22 Apr 201607:00:36 22 Apr 20165 minutes 35 seconds
Read alignment to reference genome07:00:36 22 Apr 201607:16:32 22 Apr 201615 minutes 56 seconds
Preprocessing alignments for candidate junction identification07:16:32 22 Apr 201607:27:06 22 Apr 201610 minutes 34 seconds
Preliminary analysis of coverage distribution07:27:06 22 Apr 201607:41:34 22 Apr 201614 minutes 28 seconds
Identifying junction candidates07:41:34 22 Apr 201607:41:37 22 Apr 20163 seconds
Re-alignment to junction candidates07:41:37 22 Apr 201607:45:11 22 Apr 20163 minutes 34 seconds
Resolving alignments with junction candidates07:45:11 22 Apr 201608:01:13 22 Apr 201616 minutes 2 seconds
Creating BAM files08:01:13 22 Apr 201608:11:53 22 Apr 201610 minutes 40 seconds
Tabulating error counts08:11:53 22 Apr 201608:22:54 22 Apr 201611 minutes 1 second
Re-calibrating base error rates08:22:54 22 Apr 201608:22:57 22 Apr 20163 seconds
Examining read alignment evidence08:22:57 22 Apr 201610:05:15 22 Apr 20161 hour 42 minutes 18 seconds
Polymorphism statistics10:05:15 22 Apr 201610:05:17 22 Apr 20162 seconds
Output10:05:17 22 Apr 201610:07:26 22 Apr 20162 minutes 9 seconds
Total 3 hours 12 minutes 25 seconds