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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL043_S43_R1_001.good.fq3,887,534494,077,940100.0%127.1 bases128 bases99.5%
errorsPAL043_S43_R2_001.good.fq3,887,534494,077,940100.0%127.1 bases128 bases98.7%
total7,775,068988,155,880100.0%127.1 bases128 bases99.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3791817.117.3100.0%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≤ 10000011984
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 ≤ 5000177
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.087

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.04479

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 input21:04:02 14 Nov 201721:05:38 14 Nov 20171 minute 36 seconds
Read alignment to reference genome21:05:38 14 Nov 201721:10:15 14 Nov 20174 minutes 37 seconds
Preprocessing alignments for candidate junction identification21:10:15 14 Nov 201721:13:04 14 Nov 20172 minutes 49 seconds
Preliminary analysis of coverage distribution21:13:04 14 Nov 201721:17:26 14 Nov 20174 minutes 22 seconds
Identifying junction candidates21:17:26 14 Nov 201721:17:35 14 Nov 20179 seconds
Re-alignment to junction candidates21:17:35 14 Nov 201721:18:47 14 Nov 20171 minute 12 seconds
Resolving alignments with junction candidates21:18:47 14 Nov 201721:24:05 14 Nov 20175 minutes 18 seconds
Creating BAM files21:24:05 14 Nov 201721:26:37 14 Nov 20172 minutes 32 seconds
Tabulating error counts21:26:37 14 Nov 201721:31:01 14 Nov 20174 minutes 24 seconds
Re-calibrating base error rates21:31:01 14 Nov 201721:31:03 14 Nov 20172 seconds
Examining read alignment evidence21:31:03 14 Nov 201722:03:14 14 Nov 201732 minutes 11 seconds
Polymorphism statistics22:03:14 14 Nov 201722:03:17 14 Nov 20173 seconds
Output22:03:17 14 Nov 201722:04:20 14 Nov 20171 minute 3 seconds
Total 1 hour 18 seconds