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-COUM3-10_S7_L001_R1_0011,181,211177,701,725100.0%150.4 bases151 bases99.7%
errorsqtrim-COUM3-10_S7_L001_R2_0011,180,874177,409,133100.0%150.2 bases151 bases97.6%
total2,362,085355,110,858100.0%150.3 bases151 bases98.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65275.61.498.3%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≤ 1000002977
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_0009130.78828

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 input14:39:54 03 Jan 201714:40:53 03 Jan 201759 seconds
Read alignment to reference genome14:40:54 03 Jan 201714:48:14 03 Jan 20177 minutes 20 seconds
Preprocessing alignments for candidate junction identification14:48:14 03 Jan 201714:49:42 03 Jan 20171 minute 28 seconds
Preliminary analysis of coverage distribution14:49:42 03 Jan 201714:52:19 03 Jan 20172 minutes 37 seconds
Identifying junction candidates14:52:19 03 Jan 201714:52:19 03 Jan 20170 seconds
Re-alignment to junction candidates14:52:19 03 Jan 201714:53:58 03 Jan 20171 minute 39 seconds
Resolving alignments with junction candidates14:53:58 03 Jan 201714:56:14 03 Jan 20172 minutes 16 seconds
Creating BAM files14:56:14 03 Jan 201714:58:01 03 Jan 20171 minute 47 seconds
Tabulating error counts14:58:01 03 Jan 201715:00:07 03 Jan 20172 minutes 6 seconds
Re-calibrating base error rates15:00:07 03 Jan 201715:00:08 03 Jan 20171 second
Examining read alignment evidence15:00:08 03 Jan 201715:17:12 03 Jan 201717 minutes 4 seconds
Polymorphism statistics15:17:12 03 Jan 201715:17:13 03 Jan 20171 second
Output15:17:13 03 Jan 201715:17:35 03 Jan 201722 seconds
Total 37 minutes 40 seconds