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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsA_end_LSM_A12_F70_I3_S135_L004_R1_001.good.fq2,879,508285,661,181100.0%99.2 bases101 bases96.6%
errorsA_end_LSM_A12_F70_I3_S135_L004_R2_001.good.fq2,879,507285,661,080100.0%99.2 bases101 bases95.8%
total5,759,015571,322,261100.0%99.2 bases101 bases96.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionJE3692-46,192,17789.32.7100.0%Pseudomonas putida KT2440 complete genome.
total6,192,177100.0%

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≤ 100000100024
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 ≤ 50001539
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.052

Junction Skew Score Calculation

reference sequencepr(no read start)
JE3692-40.68696

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 input20:12:09 01 Feb 202420:14:10 01 Feb 20242 minutes 1 second
Read alignment to reference genome20:14:10 01 Feb 202420:28:09 01 Feb 202413 minutes 59 seconds
Preprocessing alignments for candidate junction identification20:28:09 01 Feb 202420:29:17 01 Feb 20241 minute 8 seconds
Preliminary analysis of coverage distribution20:29:17 01 Feb 202420:30:55 01 Feb 20241 minute 38 seconds
Identifying junction candidates20:30:55 01 Feb 202420:31:07 01 Feb 202412 seconds
Re-alignment to junction candidates20:31:07 01 Feb 202420:34:09 01 Feb 20243 minutes 2 seconds
Resolving best read alignments20:34:09 01 Feb 202420:35:45 01 Feb 20241 minute 36 seconds
Creating BAM files20:35:46 01 Feb 202420:37:12 01 Feb 20241 minute 26 seconds
Tabulating error counts20:37:12 01 Feb 202420:38:01 01 Feb 202449 seconds
Re-calibrating base error rates20:38:01 01 Feb 202420:38:02 01 Feb 20241 second
Examining read alignment evidence20:38:02 01 Feb 202420:47:58 01 Feb 20249 minutes 56 seconds
Polymorphism statistics20:47:58 01 Feb 202420:47:59 01 Feb 20241 second
Output20:47:59 01 Feb 202420:48:23 01 Feb 202424 seconds
Total 36 minutes 13 seconds