breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL22_S30_L002_R2_0011,612,450242,688,80399.7%150.5 bases151 bases97.6%
errorsALE-IL22_S30_L002_R1_0011,608,684242,133,44599.5%150.5 bases151 bases99.2%
errorsALE-IL22_S30_L001_R1_0011,618,091243,531,69699.4%150.5 bases151 bases99.2%
errorsALE-IL22_S30_L003_R1_0011,638,199246,588,32399.7%150.5 bases151 bases98.9%
errorsALE-IL22_S30_L004_R2_0011,634,601246,036,30899.8%150.5 bases151 bases98.0%
errorsALE-IL22_S30_L003_R2_0011,639,992246,827,75499.8%150.5 bases151 bases97.1%
errorsALE-IL22_S30_L001_R2_0011,622,152244,136,84199.7%150.5 bases151 bases97.4%
errorsALE-IL22_S30_L004_R1_0011,634,482246,037,81299.8%150.5 bases151 bases99.2%
total13,008,6511,957,980,98299.7%150.5 bases151 bases98.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652413.94.9100.0%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≤ 1000009633
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 ≤ 5000215
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.014

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.34633

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 cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
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

Execution Times

stepstartendelapsed
Read and reference sequence file input15:55:27 21 Apr 201616:00:47 21 Apr 20165 minutes 20 seconds
Read alignment to reference genome16:00:47 21 Apr 201616:14:29 21 Apr 201613 minutes 42 seconds
Preprocessing alignments for candidate junction identification16:14:29 21 Apr 201616:20:41 21 Apr 20166 minutes 12 seconds
Preliminary analysis of coverage distribution16:20:41 21 Apr 201616:37:57 21 Apr 201617 minutes 16 seconds
Identifying junction candidates16:37:57 21 Apr 201616:38:00 21 Apr 20163 seconds
Re-alignment to junction candidates16:38:00 21 Apr 201616:42:49 21 Apr 20164 minutes 49 seconds
Resolving alignments with junction candidates16:42:49 21 Apr 201617:02:01 21 Apr 201619 minutes 12 seconds
Creating BAM files17:02:01 21 Apr 201617:13:12 21 Apr 201611 minutes 11 seconds
Tabulating error counts17:13:12 21 Apr 201617:31:03 21 Apr 201617 minutes 51 seconds
Re-calibrating base error rates17:31:03 21 Apr 201617:31:11 21 Apr 20168 seconds
Examining read alignment evidence17:31:11 21 Apr 201619:20:33 21 Apr 20161 hour 49 minutes 22 seconds
Polymorphism statistics19:20:33 21 Apr 201619:20:37 21 Apr 20164 seconds
Output19:20:37 21 Apr 201619:22:24 21 Apr 20161 minute 47 seconds
Total 3 hours 26 minutes 57 seconds