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_160_S148_L001_R1_001.good.fq6,004,317873,648,576100.0%145.5 bases150 bases96.3%
errorsPputida_PALE__HGL_Pputida_160_S148_L001_R2_001.good.fq6,004,317873,648,576100.0%145.5 bases150 bases95.7%
total12,008,6341,747,297,152100.0%145.5 bases150 bases96.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,186,878201.87.9100.0%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≤ 100000100000
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 ≤ 50001044
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.052

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.53667

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 input11:31:26 04 Apr 202011:34:29 04 Apr 20203 minutes 3 seconds
Read alignment to reference genome11:34:30 04 Apr 202012:00:31 04 Apr 202026 minutes 1 second
Preprocessing alignments for candidate junction identification12:00:31 04 Apr 202012:03:28 04 Apr 20202 minutes 57 seconds
Preliminary analysis of coverage distribution12:03:28 04 Apr 202012:08:47 04 Apr 20205 minutes 19 seconds
Identifying junction candidates12:08:47 04 Apr 202012:15:14 04 Apr 20206 minutes 27 seconds
Re-alignment to junction candidates12:15:14 04 Apr 202012:22:18 04 Apr 20207 minutes 4 seconds
Resolving best read alignments12:22:18 04 Apr 202012:27:56 04 Apr 20205 minutes 38 seconds
Creating BAM files12:27:56 04 Apr 202012:32:35 04 Apr 20204 minutes 39 seconds
Tabulating error counts12:32:35 04 Apr 202012:35:12 04 Apr 20202 minutes 37 seconds
Re-calibrating base error rates12:35:12 04 Apr 202012:35:13 04 Apr 20201 second
Examining read alignment evidence12:35:13 04 Apr 202013:00:15 04 Apr 202025 minutes 2 seconds
Polymorphism statistics13:00:15 04 Apr 202013:00:23 04 Apr 20208 seconds
Output13:00:23 04 Apr 202013:01:28 04 Apr 20201 minute 5 seconds
Total 1 hour 30 minutes 1 second