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_HGL_15_S336_L002_R1_001.good.fq565,02678,456,373100.0%138.9 bases150 bases95.8%
errorsPputida_HGL_15_S336_L002_R2_001.good.fq565,02678,456,373100.0%138.9 bases150 bases93.4%
total1,130,052156,912,746100.0%138.9 bases150 bases94.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92924.23.3100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,181,929100.0%

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≤ 10000011456
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 ≤ 500048
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.92144

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input14:13:04 06 Apr 202014:13:23 06 Apr 202019 seconds
Read alignment to reference genome14:13:24 06 Apr 202014:16:07 06 Apr 20202 minutes 43 seconds
Preprocessing alignments for candidate junction identification14:16:07 06 Apr 202014:16:22 06 Apr 202015 seconds
Preliminary analysis of coverage distribution14:16:22 06 Apr 202014:16:57 06 Apr 202035 seconds
Identifying junction candidates14:16:57 06 Apr 202014:17:03 06 Apr 20206 seconds
Re-alignment to junction candidates14:17:03 06 Apr 202014:17:34 06 Apr 202031 seconds
Resolving best read alignments14:17:34 06 Apr 202014:18:00 06 Apr 202026 seconds
Creating BAM files14:18:00 06 Apr 202014:18:32 06 Apr 202032 seconds
Tabulating error counts14:18:32 06 Apr 202014:18:44 06 Apr 202012 seconds
Re-calibrating base error rates14:18:44 06 Apr 202014:18:45 06 Apr 20201 second
Examining read alignment evidence14:18:45 06 Apr 202014:24:30 06 Apr 20205 minutes 45 seconds
Polymorphism statistics14:24:30 06 Apr 202014:24:30 06 Apr 20200 seconds
Output14:24:30 06 Apr 202014:24:55 06 Apr 202025 seconds
Total 11 minutes 50 seconds