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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL033_S33_R2_001.good.fq10,505,5931,334,607,717100.0%127.0 bases128 bases98.5%
errorsPAL033_S33_R1_001.good.fq10,505,5931,334,607,717100.0%127.0 bases128 bases99.3%
total21,011,1862,669,215,434100.0%127.0 bases128 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP016816543,3794936.786.1100.0%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≤ 10000059210
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 10
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000165
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.081

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0168160.00428

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 input09:45:08 14 Nov 201709:49:19 14 Nov 20174 minutes 11 seconds
Read alignment to reference genome09:49:19 14 Nov 201710:01:34 14 Nov 201712 minutes 15 seconds
Preprocessing alignments for candidate junction identification10:01:34 14 Nov 201710:09:00 14 Nov 20177 minutes 26 seconds
Preliminary analysis of coverage distribution10:09:00 14 Nov 201710:21:00 14 Nov 201712 minutes 0 seconds
Identifying junction candidates10:21:00 14 Nov 201710:21:12 14 Nov 201712 seconds
Re-alignment to junction candidates10:21:12 14 Nov 201710:25:10 14 Nov 20173 minutes 58 seconds
Resolving alignments with junction candidates10:25:10 14 Nov 201710:39:28 14 Nov 201714 minutes 18 seconds
Creating BAM files10:39:28 14 Nov 201710:46:31 14 Nov 20177 minutes 3 seconds
Tabulating error counts10:46:31 14 Nov 201710:58:45 14 Nov 201712 minutes 14 seconds
Re-calibrating base error rates10:58:46 14 Nov 201710:58:49 14 Nov 20173 seconds
Examining read alignment evidence10:58:49 14 Nov 201712:26:57 14 Nov 20171 hour 28 minutes 8 seconds
Polymorphism statistics12:26:57 14 Nov 201712:27:07 14 Nov 201710 seconds
Output12:27:07 14 Nov 201712:29:42 14 Nov 20172 minutes 35 seconds
Total 2 hours 44 minutes 33 seconds