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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsCCK_Evo02EP_Isolate_2_S1592_L005_R1_001.good.fq1,015,131143,262,073100.0%141.1 bases143 bases95.6%
errorsCCK_Evo02EP_Isolate_2_S1592_L005_R2_001.good.fq1,015,131143,262,073100.0%141.1 bases143 bases87.0%
total2,030,262286,524,146100.0%141.1 bases143 bases91.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65256.11.6100.0%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≤ 10000012692
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000635
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.041

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84508

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 input22:50:03 25 Feb 202022:50:34 25 Feb 202031 seconds
Read alignment to reference genome22:50:34 25 Feb 202022:56:42 25 Feb 20206 minutes 8 seconds
Preprocessing alignments for candidate junction identification22:56:42 25 Feb 202022:57:12 25 Feb 202030 seconds
Preliminary analysis of coverage distribution22:57:12 25 Feb 202022:58:16 25 Feb 20201 minute 4 seconds
Identifying junction candidates22:58:16 25 Feb 202022:58:24 25 Feb 20208 seconds
Re-alignment to junction candidates22:58:24 25 Feb 202023:00:04 25 Feb 20201 minute 40 seconds
Resolving best read alignments23:00:04 25 Feb 202023:00:47 25 Feb 202043 seconds
Creating BAM files23:00:47 25 Feb 202023:01:45 25 Feb 202058 seconds
Tabulating error counts23:01:45 25 Feb 202023:02:05 25 Feb 202020 seconds
Re-calibrating base error rates23:02:05 25 Feb 202023:02:06 25 Feb 20201 second
Examining read alignment evidence23:02:06 25 Feb 202023:06:22 25 Feb 20204 minutes 16 seconds
Polymorphism statistics23:06:22 25 Feb 202023:06:22 25 Feb 20200 seconds
Output23:06:22 25 Feb 202023:06:37 25 Feb 202015 seconds
Total 16 minutes 34 seconds