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-IL25_S33_L003_R1_0011,736,958261,500,92699.8%150.6 bases151 bases99.4%
errorsALE-IL25_S33_L002_R2_0011,711,287257,620,08699.6%150.5 bases151 bases97.9%
errorsALE-IL25_S33_L001_R1_0011,720,946259,070,15899.7%150.5 bases151 bases99.5%
errorsALE-IL25_S33_L001_R2_0011,719,060258,778,37499.6%150.5 bases151 bases97.8%
errorsALE-IL25_S33_L002_R1_0011,713,054257,898,84899.7%150.5 bases151 bases99.5%
errorsALE-IL25_S33_L003_R2_0011,734,914261,162,70599.7%150.5 bases151 bases97.5%
errorsALE-IL25_S33_L004_R2_0011,730,832260,579,01299.7%150.6 bases151 bases98.1%
errorsALE-IL25_S33_L004_R1_0011,733,862261,055,37899.8%150.6 bases151 bases99.5%
total13,800,9132,077,665,48799.7%150.5 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652441.13.5100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.

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

Number of alignment pairs examined for constructing junction candidates≤ 10000031242
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 ≤ 5000213
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.014

Junction Skew Score Calculation

reference sequencepr(no read start)

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

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

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

Read and reference sequence file input01:46:32 22 Apr 201601:52:24 22 Apr 20165 minutes 52 seconds
Read alignment to reference genome01:52:25 22 Apr 201602:04:24 22 Apr 201611 minutes 59 seconds
Preprocessing alignments for candidate junction identification02:04:24 22 Apr 201602:10:27 22 Apr 20166 minutes 3 seconds
Preliminary analysis of coverage distribution02:10:27 22 Apr 201602:27:48 22 Apr 201617 minutes 21 seconds
Identifying junction candidates02:27:48 22 Apr 201602:27:56 22 Apr 20168 seconds
Re-alignment to junction candidates02:27:56 22 Apr 201602:32:24 22 Apr 20164 minutes 28 seconds
Resolving alignments with junction candidates02:32:24 22 Apr 201602:57:20 22 Apr 201624 minutes 56 seconds
Creating BAM files02:57:20 22 Apr 201603:07:44 22 Apr 201610 minutes 24 seconds
Tabulating error counts03:07:44 22 Apr 201603:20:59 22 Apr 201613 minutes 15 seconds
Re-calibrating base error rates03:20:59 22 Apr 201603:21:01 22 Apr 20162 seconds
Examining read alignment evidence03:21:01 22 Apr 201605:14:51 22 Apr 20161 hour 53 minutes 50 seconds
Polymorphism statistics05:14:51 22 Apr 201605:14:54 22 Apr 20163 seconds
Output05:14:54 22 Apr 201605:17:23 22 Apr 20162 minutes 29 seconds
Total 3 hours 30 minutes 50 seconds