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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_PALE__HGL_Pputida_155_S143_L001_R1_001.good.fq11,703,9561,672,134,528100.0%142.9 bases150 bases93.6%
errorsPputida_PALE__HGL_Pputida_155_S143_L001_R2_001.good.fq11,703,9561,672,134,528100.0%142.9 bases150 bases93.1%
total23,407,9123,344,269,056100.0%142.9 bases150 bases93.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,186,878500.99.0100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,186,878100.0%

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≤ 100000100078
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 ≤ 50001832
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.091

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.34246

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 input18:32:53 03 Apr 202018:39:29 03 Apr 20206 minutes 36 seconds
Read alignment to reference genome18:39:30 03 Apr 202019:40:07 03 Apr 20201 hour 37 seconds
Preprocessing alignments for candidate junction identification19:40:07 03 Apr 202019:46:49 03 Apr 20206 minutes 42 seconds
Preliminary analysis of coverage distribution19:46:49 03 Apr 202019:57:14 03 Apr 202010 minutes 25 seconds
Identifying junction candidates19:57:14 03 Apr 202019:58:41 03 Apr 20201 minute 27 seconds
Re-alignment to junction candidates19:58:41 03 Apr 202020:16:30 03 Apr 202017 minutes 49 seconds
Resolving best read alignments20:16:30 03 Apr 202020:31:41 03 Apr 202015 minutes 11 seconds
Creating BAM files20:31:41 03 Apr 202020:41:09 03 Apr 20209 minutes 28 seconds
Tabulating error counts20:41:09 03 Apr 202020:46:51 03 Apr 20205 minutes 42 seconds
Re-calibrating base error rates20:46:51 03 Apr 202020:46:52 03 Apr 20201 second
Examining read alignment evidence20:46:52 03 Apr 202021:36:10 03 Apr 202049 minutes 18 seconds
Polymorphism statistics21:36:10 03 Apr 202021:36:42 03 Apr 202032 seconds
Output21:36:43 03 Apr 202021:39:32 03 Apr 20202 minutes 49 seconds
Total 3 hours 6 minutes 37 seconds