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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsLC040_JJ305_S4_L001_R1_001756,072227,577,672100.0%301.0 bases301 bases90.7%
errorsLC040_JJ305_S4_L001_R2_001755,747227,479,847100.0%301.0 bases301 bases82.4%
total1,511,819455,057,519100.0%301.0 bases301 bases86.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAE0154516,181,87359.84.0100.0%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≤ 1000004389
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 ≤ 5000217
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.021

Junction Skew Score Calculation

reference sequencepr(no read start)
AE0154510.92209

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 input15:51:05 06 Oct 202115:51:38 06 Oct 202133 seconds
Read alignment to reference genome15:51:39 06 Oct 202115:54:26 06 Oct 20212 minutes 47 seconds
Preprocessing alignments for candidate junction identification15:54:26 06 Oct 202115:54:57 06 Oct 202131 seconds
Preliminary analysis of coverage distribution15:54:57 06 Oct 202115:56:25 06 Oct 20211 minute 28 seconds
Identifying junction candidates15:56:25 06 Oct 202115:56:31 06 Oct 20216 seconds
Re-alignment to junction candidates15:56:31 06 Oct 202115:56:46 06 Oct 202115 seconds
Resolving best read alignments15:56:46 06 Oct 202115:57:18 06 Oct 202132 seconds
Creating BAM files15:57:18 06 Oct 202115:58:11 06 Oct 202153 seconds
Tabulating error counts15:58:11 06 Oct 202115:58:52 06 Oct 202141 seconds
Re-calibrating base error rates15:58:52 06 Oct 202115:58:53 06 Oct 20211 second
Examining read alignment evidence15:58:53 06 Oct 202116:09:33 06 Oct 202110 minutes 40 seconds
Polymorphism statistics16:09:33 06 Oct 202116:09:34 06 Oct 20211 second
Output16:09:34 06 Oct 202116:09:53 06 Oct 202119 seconds
Total 18 minutes 47 seconds