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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsAR_E1_GTTTCG_L005_R2_0011,591,620160,753,62099.0%101.0 bases101 bases98.2%
errorsAR_E1_GTTTCG_L005_R1_001_1162,55316,417,853100.0%101.0 bases101 bases97.5%
errorsAR_E1_GTTTCG_L005_R1_0011,608,188162,426,988100.0%101.0 bases101 bases99.1%
errorsAR_E1_GTTTCG_L005_R2_001_1162,42316,404,72399.9%101.0 bases101 bases93.3%
total3,524,784356,003,18499.5%101.0 bases101 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0077794,646,33250.55.463.2%Escherichia coli str. K-12 substr. W3110, complete genome.
coveragedistributionGFP_Plasmid_Sequ3,11513180.14.236.8%E3 plasmid sequence constructed from hi-seq reads (velvet,
total4,649,447100.0%

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≤ 10000036636
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 ≤ 500049
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0077790.80903
GFP_Plasmid_Sequ0.03193

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
bowtie22.3.4.1
R4.0.0

Execution Times

stepstartendelapsed
Read and reference sequence file input06:47:24 20 Jul 202106:49:03 20 Jul 20211 minute 39 seconds
Read alignment to reference genome06:49:03 20 Jul 202106:50:35 20 Jul 20211 minute 32 seconds
Preprocessing alignments for candidate junction identification06:50:35 20 Jul 202106:51:45 20 Jul 20211 minute 10 seconds
Preliminary analysis of coverage distribution06:51:45 20 Jul 202106:53:04 20 Jul 20211 minute 19 seconds
Identifying junction candidates06:53:04 20 Jul 202106:53:05 20 Jul 20211 second
Re-alignment to junction candidates06:53:05 20 Jul 202106:53:26 20 Jul 202121 seconds
Resolving best read alignments06:53:26 20 Jul 202106:55:08 20 Jul 20211 minute 42 seconds
Creating BAM files06:55:08 20 Jul 202106:56:09 20 Jul 20211 minute 1 second
Tabulating error counts06:56:09 20 Jul 202106:56:45 20 Jul 202136 seconds
Re-calibrating base error rates06:56:45 20 Jul 202106:56:48 20 Jul 20213 seconds
Examining read alignment evidence06:56:48 20 Jul 202107:00:26 20 Jul 20213 minutes 38 seconds
Polymorphism statistics07:00:26 20 Jul 202107:00:29 20 Jul 20213 seconds
Output07:00:29 20 Jul 202107:00:53 20 Jul 202124 seconds
Output :: Mutation Prediction07:00:29 20 Jul 202107:00:35 20 Jul 20216 seconds
Output :: Mutation Annotation07:00:35 20 Jul 202107:00:35 20 Jul 20210 seconds
Total 13 minutes 35 seconds