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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJBEI_Galactose_A34_F6_I4_S9_R1_001.good.fq419,94655,889,982100.0%133.1 bases136 bases96.0%
errorsJBEI_Galactose_A34_F6_I4_S9_R2_001.good.fq419,94655,889,982100.0%133.1 bases136 bases82.5%
total839,892111,779,964100.0%133.1 bases136 bases89.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,186,87814.25.1100.0%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≤ 1000003315
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 ≤ 5000102
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.95380

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 input06:26:44 19 Jul 202006:27:07 19 Jul 202023 seconds
Read alignment to reference genome06:27:08 19 Jul 202006:29:05 19 Jul 20201 minute 57 seconds
Preprocessing alignments for candidate junction identification06:29:05 19 Jul 202006:29:26 19 Jul 202021 seconds
Preliminary analysis of coverage distribution06:29:26 19 Jul 202006:29:52 19 Jul 202026 seconds
Identifying junction candidates06:29:52 19 Jul 202006:29:53 19 Jul 20201 second
Re-alignment to junction candidates06:29:53 19 Jul 202006:30:19 19 Jul 202026 seconds
Resolving best read alignments06:30:19 19 Jul 202006:30:50 19 Jul 202031 seconds
Creating BAM files06:30:50 19 Jul 202006:31:12 19 Jul 202022 seconds
Tabulating error counts06:31:12 19 Jul 202006:31:27 19 Jul 202015 seconds
Re-calibrating base error rates06:31:27 19 Jul 202006:31:29 19 Jul 20202 seconds
Examining read alignment evidence06:31:29 19 Jul 202006:34:49 19 Jul 20203 minutes 20 seconds
Polymorphism statistics06:34:49 19 Jul 202006:34:52 19 Jul 20203 seconds
Output06:34:52 19 Jul 202006:39:56 19 Jul 20205 minutes 4 seconds
Total 13 minutes 11 seconds