breseq  version 0.39.0  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsME9041_S24_L001_R1_0012,317,205520,808,177100.0%224.8 bases251 bases95.4%
errorsME9041_S24_L001_R2_0012,317,199522,454,381100.0%225.5 bases251 bases93.0%
total4,634,4041,043,262,558100.0%225.1 bases251 bases94.2%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionNC_0009134,641,652220.815.4100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

fit relative_variance 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≤ 10000016601
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 ≤ 5000618
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.068

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.65242

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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 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
bowtie22.5.1
R4.0.3

Execution Times

stepstartendelapsed
Read and reference sequence file input16:07:30 19 Dec 202416:08:35 19 Dec 20241 minute 5 seconds
Read alignment to reference genome16:08:35 19 Dec 202416:11:24 19 Dec 20242 minutes 49 seconds
Preprocessing alignments for candidate junction identification16:11:24 19 Dec 202416:12:23 19 Dec 202459 seconds
Preliminary analysis of coverage distribution16:12:23 19 Dec 202416:15:50 19 Dec 20243 minutes 27 seconds
Identifying junction candidates16:15:50 19 Dec 202416:16:06 19 Dec 202416 seconds
Re-alignment to junction candidates16:16:06 19 Dec 202416:16:51 19 Dec 202445 seconds
Resolving best read alignments16:16:51 19 Dec 202416:18:41 19 Dec 20241 minute 50 seconds
Creating BAM files16:18:41 19 Dec 202416:21:42 19 Dec 20243 minutes 1 second
Tabulating error counts16:21:42 19 Dec 202416:23:17 19 Dec 20241 minute 35 seconds
Re-calibrating base error rates16:23:17 19 Dec 202416:23:17 19 Dec 20240 seconds
Examining read alignment evidence16:23:17 19 Dec 202416:35:29 19 Dec 202412 minutes 12 seconds
Polymorphism statistics16:35:29 19 Dec 202416:35:30 19 Dec 20241 second
Output16:35:30 19 Dec 202416:35:50 19 Dec 202420 seconds
Output :: Mutation Prediction16:35:30 19 Dec 202416:35:31 19 Dec 20241 second
Output :: Mutation Annotation16:35:31 19 Dec 202416:35:31 19 Dec 20240 seconds
Total 28 minutes 21 seconds