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_sdhCBEvo02EP_Isolate_2_S1594_L005_R1_001.good.fq955,810136,302,107100.0%142.6 bases143 bases95.5%
errorsCCK_sdhCBEvo02EP_Isolate_2_S1594_L005_R2_001.good.fq955,810136,302,107100.0%142.6 bases143 bases86.4%
total1,911,620272,604,214100.0%142.6 bases143 bases90.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65253.21.7100.0%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≤ 1000008819
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 ≤ 5000150
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.009

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.85545

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 input00:31:46 28 Feb 202000:32:15 28 Feb 202029 seconds
Read alignment to reference genome00:32:15 28 Feb 202000:38:14 28 Feb 20205 minutes 59 seconds
Preprocessing alignments for candidate junction identification00:38:14 28 Feb 202000:38:41 28 Feb 202027 seconds
Preliminary analysis of coverage distribution00:38:41 28 Feb 202000:39:42 28 Feb 20201 minute 1 second
Identifying junction candidates00:39:42 28 Feb 202000:39:44 28 Feb 20202 seconds
Re-alignment to junction candidates00:39:44 28 Feb 202000:41:11 28 Feb 20201 minute 27 seconds
Resolving best read alignments00:41:11 28 Feb 202000:41:51 28 Feb 202040 seconds
Creating BAM files00:41:51 28 Feb 202000:42:46 28 Feb 202055 seconds
Tabulating error counts00:42:46 28 Feb 202000:43:05 28 Feb 202019 seconds
Re-calibrating base error rates00:43:05 28 Feb 202000:43:06 28 Feb 20201 second
Examining read alignment evidence00:43:06 28 Feb 202000:47:10 28 Feb 20204 minutes 4 seconds
Polymorphism statistics00:47:10 28 Feb 202000:47:10 28 Feb 20200 seconds
Output00:47:10 28 Feb 202000:47:23 28 Feb 202013 seconds
Total 15 minutes 37 seconds