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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsGlu_KHP_A6_F406_I3_R1_S28_L008_R1_001.good.fq3,484,211344,936,889100.0%99.0 bases99 bases94.0%
errorsGlu_KHP_A6_F406_I3_R1_S28_L008_R2_001.good.fq3,428,392339,410,808100.0%99.0 bases99 bases90.9%
total6,912,603684,347,697100.0%99.0 bases99 bases92.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652135.23.4100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 100000100001
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50002084
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.092

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.56810

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 input12:05:05 23 May 201912:06:13 23 May 20191 minute 8 seconds
Read alignment to reference genome12:06:14 23 May 201912:18:34 23 May 201912 minutes 20 seconds
Preprocessing alignments for candidate junction identification12:18:34 23 May 201912:20:01 23 May 20191 minute 27 seconds
Preliminary analysis of coverage distribution12:20:01 23 May 201912:22:41 23 May 20192 minutes 40 seconds
Identifying junction candidates12:22:41 23 May 201912:35:20 23 May 201912 minutes 39 seconds
Re-alignment to junction candidates12:35:20 23 May 201912:39:58 23 May 20194 minutes 38 seconds
Resolving best read alignments12:39:58 23 May 201912:42:10 23 May 20192 minutes 12 seconds
Creating BAM files12:42:10 23 May 201912:44:37 23 May 20192 minutes 27 seconds
Tabulating error counts12:44:37 23 May 201912:45:33 23 May 201956 seconds
Re-calibrating base error rates12:45:33 23 May 201912:45:33 23 May 20190 seconds
Examining read alignment evidence12:45:33 23 May 201912:55:19 23 May 20199 minutes 46 seconds
Polymorphism statistics12:55:19 23 May 201912:55:22 23 May 20193 seconds
Output12:55:22 23 May 201912:56:49 23 May 20191 minute 27 seconds
Total 51 minutes 43 seconds