breseq  version 0.31.0  revision 69e7c3c0fa11
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL041_S41_R1_001.good.fq3,977,144504,754,200100.0%126.9 bases128 bases99.0%
errorsPAL041_S41_R2_001.good.fq3,977,144504,754,200100.0%126.9 bases128 bases97.8%
total7,954,2881,009,508,400100.0%126.9 bases128 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3791846.314.3100.0%Synthetic bacterium JCVI-Syn3.0 strain 6d, complete genome.
total543,379100.0%

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≤ 10000028477
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 6
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000184
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.090

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.02819

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 cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
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
bowtie22.2.8
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input09:21:24 13 Nov 201709:23:01 13 Nov 20171 minute 37 seconds
Read alignment to reference genome09:23:01 13 Nov 201709:27:42 13 Nov 20174 minutes 41 seconds
Preprocessing alignments for candidate junction identification09:27:42 13 Nov 201709:30:34 13 Nov 20172 minutes 52 seconds
Preliminary analysis of coverage distribution09:30:34 13 Nov 201709:35:12 13 Nov 20174 minutes 38 seconds
Identifying junction candidates09:35:12 13 Nov 201709:35:21 13 Nov 20179 seconds
Re-alignment to junction candidates09:35:21 13 Nov 201709:36:54 13 Nov 20171 minute 33 seconds
Resolving alignments with junction candidates09:36:54 13 Nov 201709:42:25 13 Nov 20175 minutes 31 seconds
Creating BAM files09:42:25 13 Nov 201709:44:58 13 Nov 20172 minutes 33 seconds
Tabulating error counts09:44:58 13 Nov 201709:49:25 13 Nov 20174 minutes 27 seconds
Re-calibrating base error rates09:49:25 13 Nov 201709:49:27 13 Nov 20172 seconds
Examining read alignment evidence09:49:27 13 Nov 201710:22:32 13 Nov 201733 minutes 5 seconds
Polymorphism statistics10:22:32 13 Nov 201710:22:35 13 Nov 20173 seconds
Output10:22:35 13 Nov 201710:23:35 13 Nov 20171 minute 0 seconds
Total 1 hour 2 minutes 11 seconds