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-IL26_S34_L002_R2_0011,963,400295,580,60099.7%150.5 bases151 bases97.9%
errorsALE-IL26_S34_L004_R2_0011,982,630298,486,18899.7%150.6 bases151 bases98.1%
errorsALE-IL26_S34_L002_R1_0011,961,488295,302,91999.6%150.6 bases151 bases99.4%
errorsALE-IL26_S34_L001_R1_0011,973,230297,048,88599.5%150.5 bases151 bases99.4%
errorsALE-IL26_S34_L003_R2_0011,994,556300,254,48999.8%150.5 bases151 bases97.5%
errorsALE-IL26_S34_L004_R1_0011,982,351298,461,70199.7%150.6 bases151 bases99.3%
errorsALE-IL26_S34_L003_R1_0011,993,732300,159,96999.7%150.6 bases151 bases99.2%
errorsALE-IL26_S34_L001_R2_0011,975,767297,429,46799.7%150.5 bases151 bases97.8%
total15,827,1542,382,724,21899.7%150.5 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652506.33.2100.0%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≤ 10000035163
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 ≤ 5000249
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_0009130.29156

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 input05:17:23 22 Apr 201605:24:03 22 Apr 20166 minutes 40 seconds
Read alignment to reference genome05:24:03 22 Apr 201605:37:37 22 Apr 201613 minutes 34 seconds
Preprocessing alignments for candidate junction identification05:37:37 22 Apr 201605:44:59 22 Apr 20167 minutes 22 seconds
Preliminary analysis of coverage distribution05:44:59 22 Apr 201606:01:52 22 Apr 201616 minutes 53 seconds
Identifying junction candidates06:01:52 22 Apr 201606:01:56 22 Apr 20164 seconds
Re-alignment to junction candidates06:01:56 22 Apr 201606:04:43 22 Apr 20162 minutes 47 seconds
Resolving alignments with junction candidates06:04:43 22 Apr 201606:39:45 22 Apr 201635 minutes 2 seconds
Creating BAM files06:39:45 22 Apr 201606:50:33 22 Apr 201610 minutes 48 seconds
Tabulating error counts06:50:33 22 Apr 201607:12:00 22 Apr 201621 minutes 27 seconds
Re-calibrating base error rates07:12:00 22 Apr 201607:12:05 22 Apr 20165 seconds
Examining read alignment evidence07:12:07 22 Apr 201609:11:12 22 Apr 20161 hour 59 minutes 5 seconds
Polymorphism statistics09:11:12 22 Apr 201609:11:14 22 Apr 20162 seconds
Output09:11:14 22 Apr 201609:13:26 22 Apr 20162 minutes 12 seconds
Total 3 hours 56 minutes 1 second