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-IL5_S5_L004_R2_0011,622,356244,202,71399.6%150.5 bases151 bases96.0%
errorsALE-IL5_S5_L003_R1_0011,631,622245,602,94799.6%150.5 bases151 bases98.2%
errorsALE-IL5_S5_L002_R1_0011,604,111241,454,08499.2%150.5 bases151 bases98.5%
errorsALE-IL5_S5_L002_R2_0011,610,394242,391,66399.6%150.5 bases151 bases95.6%
errorsALE-IL5_S5_L004_R1_0011,621,657244,116,13899.6%150.5 bases151 bases98.4%
errorsALE-IL5_S5_L001_R1_0011,608,895242,157,89899.1%150.5 bases151 bases98.6%
errorsALE-IL5_S5_L001_R2_0011,616,402243,278,40099.6%150.5 bases151 bases95.5%
errorsALE-IL5_S5_L003_R2_0011,632,789245,751,41599.7%150.5 bases151 bases95.3%
total12,948,2261,948,955,25899.5%150.5 bases151 bases97.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652404.83.6100.0%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≤ 1000009649
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 ≤ 5000296
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.020

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.35420

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 input18:05:31 21 Apr 201618:10:53 21 Apr 20165 minutes 22 seconds
Read alignment to reference genome18:10:53 21 Apr 201618:24:24 21 Apr 201613 minutes 31 seconds
Preprocessing alignments for candidate junction identification18:24:24 21 Apr 201618:30:49 21 Apr 20166 minutes 25 seconds
Preliminary analysis of coverage distribution18:30:49 21 Apr 201618:45:03 21 Apr 201614 minutes 14 seconds
Identifying junction candidates18:45:03 21 Apr 201618:45:05 21 Apr 20162 seconds
Re-alignment to junction candidates18:45:05 21 Apr 201618:48:05 21 Apr 20163 minutes 0 seconds
Resolving alignments with junction candidates18:48:05 21 Apr 201619:02:20 21 Apr 201614 minutes 15 seconds
Creating BAM files19:02:20 21 Apr 201619:11:41 21 Apr 20169 minutes 21 seconds
Tabulating error counts19:11:41 21 Apr 201619:26:20 21 Apr 201614 minutes 39 seconds
Re-calibrating base error rates19:26:20 21 Apr 201619:26:23 21 Apr 20163 seconds
Examining read alignment evidence19:26:23 21 Apr 201621:28:14 21 Apr 20162 hours 1 minute 51 seconds
Polymorphism statistics21:28:14 21 Apr 201621:28:17 21 Apr 20163 seconds
Output21:28:17 21 Apr 201621:30:22 21 Apr 20162 minutes 5 seconds
Total 3 hours 24 minutes 51 seconds