breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsGlu_KHP_A8_F380_I3_R1_S32_L008_R1_001.good.fq3,967,315392,764,185100.0%99.0 bases99 bases93.5%
errorsGlu_KHP_A8_F380_I3_R1_S32_L008_R2_001.good.fq3,850,383381,187,917100.0%99.0 bases99 bases88.5%
total7,817,698773,952,102100.0%99.0 bases99 bases91.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652150.72.0100.0%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≤ 100000100027
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 ≤ 50001789
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.079

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.54408

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 cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
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

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input08:55:11 23 May 201908:56:33 23 May 20191 minute 22 seconds
Read alignment to reference genome08:56:33 23 May 201909:10:58 23 May 201914 minutes 25 seconds
Preprocessing alignments for candidate junction identification09:10:58 23 May 201909:12:34 23 May 20191 minute 36 seconds
Preliminary analysis of coverage distribution09:12:34 23 May 201909:15:38 23 May 20193 minutes 4 seconds
Identifying junction candidates09:15:38 23 May 201909:27:55 23 May 201912 minutes 17 seconds
Re-alignment to junction candidates09:27:55 23 May 201909:32:47 23 May 20194 minutes 52 seconds
Resolving best read alignments09:32:47 23 May 201909:35:14 23 May 20192 minutes 27 seconds
Creating BAM files09:35:14 23 May 201909:38:01 23 May 20192 minutes 47 seconds
Tabulating error counts09:38:01 23 May 201909:39:03 23 May 20191 minute 2 seconds
Re-calibrating base error rates09:39:03 23 May 201909:39:04 23 May 20191 second
Examining read alignment evidence09:39:04 23 May 201909:49:53 23 May 201910 minutes 49 seconds
Polymorphism statistics09:49:53 23 May 201909:49:56 23 May 20193 seconds
Output09:49:56 23 May 201909:51:12 23 May 20191 minute 16 seconds
Total 56 minutes 1 second