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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL042_S42_R2_001.good.fq3,328,433423,212,561100.0%127.2 bases128 bases98.6%
errorsPAL042_S42_R1_001.good.fq3,328,433423,212,561100.0%127.2 bases128 bases99.4%
total6,656,866846,425,122100.0%127.2 bases128 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3791563.325.5100.0%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≤ 10000014060
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 ≤ 5000154
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.076

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.06646

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 input08:54:04 14 Nov 201708:55:27 14 Nov 20171 minute 23 seconds
Read alignment to reference genome08:55:27 14 Nov 201708:59:17 14 Nov 20173 minutes 50 seconds
Preprocessing alignments for candidate junction identification08:59:17 14 Nov 201709:01:41 14 Nov 20172 minutes 24 seconds
Preliminary analysis of coverage distribution09:01:41 14 Nov 201709:05:22 14 Nov 20173 minutes 41 seconds
Identifying junction candidates09:05:22 14 Nov 201709:05:31 14 Nov 20179 seconds
Re-alignment to junction candidates09:05:31 14 Nov 201709:06:30 14 Nov 201759 seconds
Resolving alignments with junction candidates09:06:30 14 Nov 201709:10:55 14 Nov 20174 minutes 25 seconds
Creating BAM files09:10:55 14 Nov 201709:13:05 14 Nov 20172 minutes 10 seconds
Tabulating error counts09:13:05 14 Nov 201709:16:50 14 Nov 20173 minutes 45 seconds
Re-calibrating base error rates09:16:50 14 Nov 201709:16:52 14 Nov 20172 seconds
Examining read alignment evidence09:16:52 14 Nov 201709:44:14 14 Nov 201727 minutes 22 seconds
Polymorphism statistics09:44:14 14 Nov 201709:44:16 14 Nov 20172 seconds
Output09:44:16 14 Nov 201709:45:07 14 Nov 201751 seconds
Total 51 minutes 3 seconds