breseq  version 0.33.2  revision caddc01d3be9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_HGL_60_S214_L002_R1_001.good.fq2,410,459322,209,903100.0%133.7 bases150 bases93.8%
errorsPputida_HGL_60_S214_L002_R2_001.good.fq2,410,459322,209,903100.0%133.7 bases150 bases91.9%
total4,820,918644,419,806100.0%133.7 bases150 bases92.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92996.72.8100.0%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≤ 10000092733
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000992
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.050

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.72847

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 input22:14:52 20 Aug 201922:16:49 20 Aug 20191 minute 57 seconds
Read alignment to reference genome22:16:50 20 Aug 201922:34:25 20 Aug 201917 minutes 35 seconds
Preprocessing alignments for candidate junction identification22:34:25 20 Aug 201922:36:09 20 Aug 20191 minute 44 seconds
Preliminary analysis of coverage distribution22:36:09 20 Aug 201922:39:32 20 Aug 20193 minutes 23 seconds
Identifying junction candidates22:39:32 20 Aug 201922:43:51 20 Aug 20194 minutes 19 seconds
Re-alignment to junction candidates22:43:51 20 Aug 201922:49:05 20 Aug 20195 minutes 14 seconds
Resolving best read alignments22:49:05 20 Aug 201922:51:41 20 Aug 20192 minutes 36 seconds
Creating BAM files22:51:41 20 Aug 201922:54:42 20 Aug 20193 minutes 1 second
Tabulating error counts22:54:42 20 Aug 201922:56:15 20 Aug 20191 minute 33 seconds
Re-calibrating base error rates22:56:15 20 Aug 201922:56:17 20 Aug 20192 seconds
Examining read alignment evidence22:56:17 20 Aug 201900:06:26 21 Aug 20191 hour 10 minutes 9 seconds
Polymorphism statistics00:06:26 21 Aug 201900:06:34 21 Aug 20198 seconds
Output00:06:34 21 Aug 201900:14:42 21 Aug 20198 minutes 8 seconds
Total 1 hour 59 minutes 49 seconds