breseq  version 0.35.5  revision 9f368df52761
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsABF028_SAMPLE10_L001_R2_001637,280191,821,280100.0%301.0 bases301 bases52.0%
errorsABF028_S10_L001_R2_001785,947236,570,047100.0%301.0 bases301 bases50.0%
errorsABF028_SAMPLE10_L001_R1_001637,282191,821,882100.0%301.0 bases301 bases52.6%
errorsABF028_S10_L001_R1_001786,231236,655,531100.0%301.0 bases301 bases52.4%
total2,846,740856,868,740100.0%301.0 bases301 bases51.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAE0154516,181,87365.74.3100.0%Pseudomonas putida KT2440 complete genome.
total6,181,873100.0%

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≤ 10000017399
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 ≤ 500049
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
AE0154510.91939

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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 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
bowtie22.4.2
R3.6.3

Execution Times

stepstartendelapsed
Read and reference sequence file input19:09:37 13 Jul 202119:10:31 13 Jul 202154 seconds
Read alignment to reference genome19:10:31 13 Jul 202119:28:46 13 Jul 202118 minutes 15 seconds
Preprocessing alignments for candidate junction identification19:28:46 13 Jul 202119:29:22 13 Jul 202136 seconds
Preliminary analysis of coverage distribution19:29:22 13 Jul 202119:30:27 13 Jul 20211 minute 5 seconds
Identifying junction candidates19:30:27 13 Jul 202119:31:29 13 Jul 20211 minute 2 seconds
Re-alignment to junction candidates19:31:29 13 Jul 202119:32:08 13 Jul 202139 seconds
Resolving best read alignments19:32:08 13 Jul 202119:33:15 13 Jul 20211 minute 7 seconds
Creating BAM files19:33:15 13 Jul 202119:34:06 13 Jul 202151 seconds
Tabulating error counts19:34:06 13 Jul 202119:34:47 13 Jul 202141 seconds
Re-calibrating base error rates19:34:47 13 Jul 202119:34:49 13 Jul 20212 seconds
Examining read alignment evidence19:34:49 13 Jul 202119:40:18 13 Jul 20215 minutes 29 seconds
Polymorphism statistics19:40:18 13 Jul 202119:40:19 13 Jul 20211 second
Output19:40:19 13 Jul 202119:40:27 13 Jul 20218 seconds
Total 30 minutes 50 seconds