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-12PD7-5_S16_L001_R1_001481,66172,202,167100.0%149.9 bases151 bases98.6%
errorsqtrim-12PD7-5_S9_L001_R1_0011,407,176211,516,251100.0%150.3 bases151 bases97.7%
errorsqtrim-12PD7-5_S9_L001_R2_0011,407,247211,420,544100.0%150.2 bases151 bases97.2%
errorsqtrim-12PD7-5_S16_L001_R2_001481,65572,152,974100.0%149.8 bases151 bases97.9%
total3,777,739567,291,936100.0%150.2 bases151 bases97.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652119.51.698.3%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≤ 1000001642
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 ≤ 500044
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.69207

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 input14:32:04 02 Jan 201714:33:25 02 Jan 20171 minute 21 seconds
Read alignment to reference genome14:33:26 02 Jan 201714:45:34 02 Jan 201712 minutes 8 seconds
Preprocessing alignments for candidate junction identification14:45:34 02 Jan 201714:47:52 02 Jan 20172 minutes 18 seconds
Preliminary analysis of coverage distribution14:47:52 02 Jan 201714:51:22 02 Jan 20173 minutes 30 seconds
Identifying junction candidates14:51:22 02 Jan 201714:51:23 02 Jan 20171 second
Re-alignment to junction candidates14:51:23 02 Jan 201714:53:40 02 Jan 20172 minutes 17 seconds
Resolving alignments with junction candidates14:53:40 02 Jan 201714:57:04 02 Jan 20173 minutes 24 seconds
Creating BAM files14:57:04 02 Jan 201714:59:39 02 Jan 20172 minutes 35 seconds
Tabulating error counts14:59:39 02 Jan 201715:02:25 02 Jan 20172 minutes 46 seconds
Re-calibrating base error rates15:02:25 02 Jan 201715:02:27 02 Jan 20172 seconds
Examining read alignment evidence15:02:27 02 Jan 201715:23:57 02 Jan 201721 minutes 30 seconds
Polymorphism statistics15:23:57 02 Jan 201715:23:59 02 Jan 20172 seconds
Output15:23:59 02 Jan 201715:24:48 02 Jan 201749 seconds
Total 52 minutes 43 seconds