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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsCCK_pgIsolate_Evo03EP_Isolate_1_S1619_L005_R1_001.good.fq734,653104,710,114100.0%142.5 bases143 bases90.1%
errorsCCK_pgIsolate_Evo03EP_Isolate_1_S1619_L005_R2_001.good.fq734,653104,710,114100.0%142.5 bases143 bases82.0%
total1,469,306209,420,228100.0%142.5 bases143 bases86.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65238.61.7100.0%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≤ 10000011084
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 ≤ 5000228
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.014

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.89406

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 input06:35:32 29 Feb 202006:35:54 29 Feb 202022 seconds
Read alignment to reference genome06:35:55 29 Feb 202006:41:15 29 Feb 20205 minutes 20 seconds
Preprocessing alignments for candidate junction identification06:41:15 29 Feb 202006:41:36 29 Feb 202021 seconds
Preliminary analysis of coverage distribution06:41:36 29 Feb 202006:42:22 29 Feb 202046 seconds
Identifying junction candidates06:42:22 29 Feb 202006:42:24 29 Feb 20202 seconds
Re-alignment to junction candidates06:42:24 29 Feb 202006:43:33 29 Feb 20201 minute 9 seconds
Resolving best read alignments06:43:33 29 Feb 202006:44:04 29 Feb 202031 seconds
Creating BAM files06:44:04 29 Feb 202006:44:46 29 Feb 202042 seconds
Tabulating error counts06:44:46 29 Feb 202006:45:00 29 Feb 202014 seconds
Re-calibrating base error rates06:45:00 29 Feb 202006:45:01 29 Feb 20201 second
Examining read alignment evidence06:45:01 29 Feb 202006:48:09 29 Feb 20203 minutes 8 seconds
Polymorphism statistics06:48:09 29 Feb 202006:48:10 29 Feb 20201 second
Output06:48:10 29 Feb 202006:48:22 29 Feb 202012 seconds
Total 12 minutes 49 seconds