breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-COUM4-5_S9_L001_R1_0011,067,223160,470,867100.0%150.4 bases151 bases98.2%
errorsqtrim-COUM4-5_S9_L001_R2_0011,066,862160,032,312100.0%150.0 bases151 bases95.0%
total2,134,085320,503,179100.0%150.2 bases151 bases96.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65266.14.798.2%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≤ 100000571
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 ≤ 500019
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81225

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 input17:02:11 03 Jan 201717:02:55 03 Jan 201744 seconds
Read alignment to reference genome17:02:56 03 Jan 201717:09:50 03 Jan 20176 minutes 54 seconds
Preprocessing alignments for candidate junction identification17:09:50 03 Jan 201717:11:01 03 Jan 20171 minute 11 seconds
Preliminary analysis of coverage distribution17:11:01 03 Jan 201717:13:03 03 Jan 20172 minutes 2 seconds
Identifying junction candidates17:13:03 03 Jan 201717:13:03 03 Jan 20170 seconds
Re-alignment to junction candidates17:13:03 03 Jan 201717:14:33 03 Jan 20171 minute 30 seconds
Resolving alignments with junction candidates17:14:33 03 Jan 201717:16:50 03 Jan 20172 minutes 17 seconds
Creating BAM files17:16:50 03 Jan 201717:18:25 03 Jan 20171 minute 35 seconds
Tabulating error counts17:18:25 03 Jan 201717:20:27 03 Jan 20172 minutes 2 seconds
Re-calibrating base error rates17:20:27 03 Jan 201717:20:28 03 Jan 20171 second
Examining read alignment evidence17:20:28 03 Jan 201717:36:13 03 Jan 201715 minutes 45 seconds
Polymorphism statistics17:36:13 03 Jan 201717:36:14 03 Jan 20171 second
Output17:36:14 03 Jan 201717:36:36 03 Jan 201722 seconds
Total 34 minutes 24 seconds