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-OCTA8-5_S19_L001_R1_0011,192,705179,392,334100.0%150.4 bases151 bases98.8%
errorsqtrim-OCTA8-5_S19_L001_R2_0011,192,676179,288,124100.0%150.3 bases151 bases98.0%
total2,385,381358,680,458100.0%150.4 bases151 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65276.11.398.3%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≤ 1000001117
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 ≤ 500021
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_0009130.78700

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 input09:19:23 02 Jan 201709:20:18 02 Jan 201755 seconds
Read alignment to reference genome09:20:19 02 Jan 201709:27:43 02 Jan 20177 minutes 24 seconds
Preprocessing alignments for candidate junction identification09:27:43 02 Jan 201709:29:04 02 Jan 20171 minute 21 seconds
Preliminary analysis of coverage distribution09:29:04 02 Jan 201709:31:23 02 Jan 20172 minutes 19 seconds
Identifying junction candidates09:31:23 02 Jan 201709:31:24 02 Jan 20171 second
Re-alignment to junction candidates09:31:24 02 Jan 201709:32:52 02 Jan 20171 minute 28 seconds
Resolving alignments with junction candidates09:32:52 02 Jan 201709:35:18 02 Jan 20172 minutes 26 seconds
Creating BAM files09:35:18 02 Jan 201709:37:01 02 Jan 20171 minute 43 seconds
Tabulating error counts09:37:01 02 Jan 201709:39:01 02 Jan 20172 minutes 0 seconds
Re-calibrating base error rates09:39:01 02 Jan 201709:39:02 02 Jan 20171 second
Examining read alignment evidence09:39:02 02 Jan 201709:53:36 02 Jan 201714 minutes 34 seconds
Polymorphism statistics09:53:36 02 Jan 201709:53:37 02 Jan 20171 second
Output09:53:37 02 Jan 201709:53:55 02 Jan 201718 seconds
Total 34 minutes 31 seconds