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-IL33_S41_L002_R1_0011,765,812265,839,80799.8%150.5 bases151 bases99.5%
errorsALE-IL33_S41_L002_R2_0011,762,891265,391,03199.6%150.5 bases151 bases97.9%
errorsALE-IL33_S41_L001_R1_0011,772,892266,892,37499.8%150.5 bases151 bases99.5%
errorsALE-IL33_S41_L001_R2_0011,770,357266,497,98899.6%150.5 bases151 bases97.8%
errorsALE-IL33_S41_L004_R1_0011,804,215271,645,16999.9%150.6 bases151 bases99.5%
errorsALE-IL33_S41_L004_R2_0011,800,796271,111,41299.7%150.6 bases151 bases98.1%
errorsALE-IL33_S41_L003_R2_0011,790,561269,547,62699.7%150.5 bases151 bases97.5%
errorsALE-IL33_S41_L003_R1_0011,793,323269,991,60799.9%150.6 bases151 bases99.4%
total14,260,8472,146,917,01499.7%150.5 bases151 bases98.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652457.57.5100.0%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≤ 1000008662
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 ≤ 5000173
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_0009130.32486

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 input08:03:44 21 Apr 201608:13:39 21 Apr 20169 minutes 55 seconds
Read alignment to reference genome08:13:40 21 Apr 201608:36:20 21 Apr 201622 minutes 40 seconds
Preprocessing alignments for candidate junction identification08:36:20 21 Apr 201608:43:17 21 Apr 20166 minutes 57 seconds
Preliminary analysis of coverage distribution08:43:17 21 Apr 201609:01:10 21 Apr 201617 minutes 53 seconds
Identifying junction candidates09:01:10 21 Apr 201609:01:14 21 Apr 20164 seconds
Re-alignment to junction candidates09:01:14 21 Apr 201609:07:41 21 Apr 20166 minutes 27 seconds
Resolving alignments with junction candidates09:07:41 21 Apr 201609:39:44 21 Apr 201632 minutes 3 seconds
Creating BAM files09:39:44 21 Apr 201609:52:34 21 Apr 201612 minutes 50 seconds
Tabulating error counts09:52:34 21 Apr 201610:06:10 21 Apr 201613 minutes 36 seconds
Re-calibrating base error rates10:06:10 21 Apr 201610:06:14 21 Apr 20164 seconds
Examining read alignment evidence10:06:14 21 Apr 201612:05:40 21 Apr 20161 hour 59 minutes 26 seconds
Polymorphism statistics12:05:40 21 Apr 201612:05:43 21 Apr 20163 seconds
Output12:05:43 21 Apr 201612:07:41 21 Apr 20161 minute 58 seconds
Total 4 hours 3 minutes 56 seconds