breseq  version 0.26.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-NXT-Ace1_S5_L001_R1_001_10252015925,490176,363,00099.9%190.6 bases200 bases99.7%
errorsSSW-NXT-Ace1_S5_L001_R1_001_10112015914,322125,820,10399.9%137.6 bases141 bases99.7%
errorsSSW-NXT-Ace1_S5_L001_R2_001_10112015914,287118,131,62599.9%129.2 bases132 bases99.0%
errorsSSW-NXT-Ace1_S5_L001_R2_001_10252015925,403134,942,33699.9%145.8 bases150 bases99.2%
total3,679,502555,257,06499.9%150.9 bases200 bases99.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652116.83.3100.0%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≤ 1000007264
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 ≤ 5000176
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.015

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.76704

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
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.1
Polymorphism minimum coverage each strand2
Polymorphism bias cutoff0.05
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 input02:45:31 28 Oct 201502:46:30 28 Oct 201559 seconds
Read alignment to reference genome02:46:31 28 Oct 201502:49:56 28 Oct 20153 minutes 25 seconds
Preprocessing alignments for candidate junction identification02:49:56 28 Oct 201502:51:26 28 Oct 20151 minute 30 seconds
Preliminary analysis of coverage distribution02:51:26 28 Oct 201502:54:36 28 Oct 20153 minutes 10 seconds
Identifying junction candidates02:54:36 28 Oct 201502:54:37 28 Oct 20151 second
Re-alignment to junction candidates02:54:37 28 Oct 201502:55:21 28 Oct 201544 seconds
Resolving alignments with junction candidates02:55:21 28 Oct 201502:59:10 28 Oct 20153 minutes 49 seconds
Creating BAM files02:59:10 28 Oct 201503:01:08 28 Oct 20151 minute 58 seconds
Tabulating error counts03:01:08 28 Oct 201503:04:40 28 Oct 20153 minutes 32 seconds
Re-calibrating base error rates03:04:40 28 Oct 201503:04:41 28 Oct 20151 second
Examining read alignment evidence03:04:41 28 Oct 201503:31:51 28 Oct 201527 minutes 10 seconds
Polymorphism statistics03:31:51 28 Oct 201503:31:51 28 Oct 20150 seconds
Output03:31:51 28 Oct 201503:33:14 28 Oct 20151 minute 23 seconds
Total 47 minutes 42 seconds