breseq  version 0.28.1  revision 52323b585d6f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL16_S20_L001_R1_0011,282,968193,177,92699.8%150.6 bases151 bases99.4%
errorsALE-IL16_S20_L001_R2_0011,280,861192,848,26099.7%150.6 bases151 bases97.8%
errorsALE-IL16_S20_L002_R1_0011,279,405192,652,05299.8%150.6 bases151 bases99.5%
errorsALE-IL16_S20_L002_R2_0011,277,039192,291,10099.7%150.6 bases151 bases97.9%
errorsALE-IL16_S20_L003_R1_0011,293,928194,842,61899.9%150.6 bases151 bases99.4%
errorsALE-IL16_S20_L003_R2_0011,292,078194,540,12899.8%150.6 bases151 bases97.5%
errorsALE-IL16_S20_L004_R1_0011,300,559195,854,11499.9%150.6 bases151 bases99.4%
errorsALE-IL16_S20_L004_R2_0011,298,159195,478,73599.7%150.6 bases151 bases98.1%
total10,304,9971,551,684,93399.8%150.6 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707330.62.898.2%Escherichia coli DH1, complete genome.
total4,630,707100.0%

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≤ 1000009828
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 ≤ 500082
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.41593

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 input15:16:51 18 Oct 201615:21:56 18 Oct 20165 minutes 5 seconds
Read alignment to reference genome15:21:57 18 Oct 201616:10:49 18 Oct 201648 minutes 52 seconds
Preprocessing alignments for candidate junction identification16:10:49 18 Oct 201616:17:22 18 Oct 20166 minutes 33 seconds
Preliminary analysis of coverage distribution16:17:22 18 Oct 201616:30:56 18 Oct 201613 minutes 34 seconds
Identifying junction candidates16:30:56 18 Oct 201616:31:04 18 Oct 20168 seconds
Re-alignment to junction candidates16:31:04 18 Oct 201616:51:42 18 Oct 201620 minutes 38 seconds
Resolving alignments with junction candidates16:51:42 18 Oct 201617:36:59 18 Oct 201645 minutes 17 seconds
Creating BAM files17:36:59 18 Oct 201617:57:26 18 Oct 201620 minutes 27 seconds
Tabulating error counts17:57:26 18 Oct 201618:07:24 18 Oct 20169 minutes 58 seconds
Re-calibrating base error rates18:07:24 18 Oct 201618:07:27 18 Oct 20163 seconds
Examining read alignment evidence18:07:27 18 Oct 201619:11:42 18 Oct 20161 hour 4 minutes 15 seconds
Polymorphism statistics19:11:42 18 Oct 201619:11:46 18 Oct 20164 seconds
Output19:11:46 18 Oct 201619:17:34 18 Oct 20165 minutes 48 seconds
Total 4 hours 42 seconds