breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors21_S21_L001_R1_001.good.fq339,23549,833,404100.0%146.9 bases149 bases98.9%
errors21_S21_L001_R2_001.good.fq339,23549,831,855100.0%146.9 bases149 bases97.6%
errors21_S21_L002_R1_001.good.fq332,19748,813,045100.0%146.9 bases149 bases98.9%
errors21_S21_L002_R2_001.good.fq332,19748,825,631100.0%147.0 bases149 bases96.9%
errors21_S21_L003_R1_001.good.fq342,45750,304,589100.0%146.9 bases149 bases99.1%
errors21_S21_L003_R2_001.good.fq342,45750,303,323100.0%146.9 bases149 bases97.8%
errors21_S21_L004_R1_001.good.fq353,28651,893,801100.0%146.9 bases149 bases99.1%
errors21_S21_L004_R2_001.good.fq353,28651,896,872100.0%146.9 bases149 bases98.1%
total2,734,350401,702,520100.0%146.9 bases149 bases98.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_002947_CJ-RC6,184,68864.32.0100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,184,688100.0%

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≤ 10000011895
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 ≤ 5000598
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.029

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_002947_CJ-RC0.82151

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 cutoff0.75
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input14:44:08 25 Oct 202414:44:57 25 Oct 202449 seconds
Read alignment to reference genome14:44:57 25 Oct 202414:50:46 25 Oct 20245 minutes 49 seconds
Preprocessing alignments for candidate junction identification14:50:46 25 Oct 202414:51:22 25 Oct 202436 seconds
Preliminary analysis of coverage distribution14:51:22 25 Oct 202414:52:58 25 Oct 20241 minute 36 seconds
Identifying junction candidates14:52:58 25 Oct 202414:53:03 25 Oct 20245 seconds
Re-alignment to junction candidates14:53:03 25 Oct 202414:54:43 25 Oct 20241 minute 40 seconds
Resolving best read alignments14:54:43 25 Oct 202414:55:35 25 Oct 202452 seconds
Creating BAM files14:55:35 25 Oct 202414:57:02 25 Oct 20241 minute 27 seconds
Tabulating error counts14:57:02 25 Oct 202414:57:39 25 Oct 202437 seconds
Re-calibrating base error rates14:57:39 25 Oct 202414:57:42 25 Oct 20243 seconds
Examining read alignment evidence14:57:42 25 Oct 202415:05:09 25 Oct 20247 minutes 27 seconds
Polymorphism statistics15:05:09 25 Oct 202415:05:09 25 Oct 20240 seconds
Output15:05:09 25 Oct 202415:05:23 25 Oct 202414 seconds
Total 21 minutes 15 seconds