breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-KHP-SSW-3-164-1-1_S11_L001_R2_0011,360,710408,583,63599.9%300.3 bases301 bases78.6%
errorsSSW-KHP-SSW-3-164-1-1_S11_L001_R1_0011,362,488409,509,516100.0%300.6 bases301 bases81.6%
total2,723,198818,093,15199.9%300.4 bases301 bases80.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652139.92.0100.0%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≤ 1000008012
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500031
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.004

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.83412

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 input17:08:57 05 Mar 201617:10:20 05 Mar 20161 minute 23 seconds
Read alignment to reference genome17:10:20 05 Mar 201617:17:32 05 Mar 20167 minutes 12 seconds
Preprocessing alignments for candidate junction identification17:17:32 05 Mar 201617:18:53 05 Mar 20161 minute 21 seconds
Preliminary analysis of coverage distribution17:18:53 05 Mar 201617:22:25 05 Mar 20163 minutes 32 seconds
Identifying junction candidates17:22:25 05 Mar 201617:22:28 05 Mar 20163 seconds
Re-alignment to junction candidates17:22:28 05 Mar 201617:23:06 05 Mar 201638 seconds
Resolving alignments with junction candidates17:23:06 05 Mar 201617:26:17 05 Mar 20163 minutes 11 seconds
Creating BAM files17:26:17 05 Mar 201617:28:20 05 Mar 20162 minutes 3 seconds
Tabulating error counts17:28:20 05 Mar 201617:31:55 05 Mar 20163 minutes 35 seconds
Re-calibrating base error rates17:31:55 05 Mar 201617:31:56 05 Mar 20161 second
Examining read alignment evidence17:31:56 05 Mar 201617:58:07 05 Mar 201626 minutes 11 seconds
Polymorphism statistics17:58:07 05 Mar 201617:58:07 05 Mar 20160 seconds
Output17:58:07 05 Mar 201617:58:41 05 Mar 201634 seconds
Total 49 minutes 44 seconds