breseq  version 0.35.7  revision b7a44cd89118
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsG2_CCGTCC_L007_R1_001503,25763,410,382100.0%126.0 bases126 bases98.1%
errorsG2_CCGTCC_L007_R2_001502,54463,320,54499.9%126.0 bases126 bases97.9%
total1,005,801126,730,92699.9%126.0 bases126 bases98.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionADP1-WT3,600,83535.11.7100.0%Acinetobacter sp. ADP1 chromosome, complete genome.

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

Number of alignment pairs examined for constructing junction candidates≤ 100000336
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 ≤ 500014
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)

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

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

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


Execution Times

Read and reference sequence file input07:49:52 20 Jul 202107:53:33 20 Jul 20213 minutes 41 seconds
Read alignment to reference genome07:56:12 20 Jul 202107:59:13 20 Jul 20213 minutes 1 second
Preprocessing alignments for candidate junction identification07:59:13 20 Jul 202108:00:21 20 Jul 20211 minute 8 seconds
Preliminary analysis of coverage distribution08:00:21 20 Jul 202108:12:20 20 Jul 202111 minutes 59 seconds
Identifying junction candidates08:12:20 20 Jul 202108:12:20 20 Jul 20210 seconds
Re-alignment to junction candidates08:12:20 20 Jul 202108:13:04 20 Jul 202144 seconds
Resolving best read alignments08:13:04 20 Jul 202108:15:08 20 Jul 20212 minutes 4 seconds
Creating BAM files08:15:08 20 Jul 202108:15:32 20 Jul 202124 seconds
Tabulating error counts08:15:32 20 Jul 202108:16:42 20 Jul 20211 minute 10 seconds
Re-calibrating base error rates08:16:42 20 Jul 202108:16:44 20 Jul 20212 seconds
Examining read alignment evidence08:16:44 20 Jul 202109:19:11 20 Jul 20211 hour 2 minutes 27 seconds
Polymorphism statistics09:19:11 20 Jul 202109:19:11 20 Jul 20210 seconds
Output09:19:11 20 Jul 202109:19:30 20 Jul 202119 seconds
Output :: Mutation Prediction09:19:11 20 Jul 202109:19:12 20 Jul 20211 second
Output :: Mutation Annotation09:19:12 20 Jul 202109:19:19 20 Jul 20217 seconds
Total 1 hour 27 minutes 7 seconds