breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-HEXA2-3_S4_L001_R1_0011,189,947179,095,908100.0%150.5 bases151 bases99.8%
errorsqtrim-HEXA2-3_S4_L001_R2_0011,189,936179,041,626100.0%150.5 bases151 bases99.4%
total2,379,883358,137,534100.0%150.5 bases151 bases99.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65275.32.198.2%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≤ 100000388
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 ≤ 500011
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.78732

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 input12:15:41 02 Jan 201712:16:28 02 Jan 201747 seconds
Read alignment to reference genome12:16:29 02 Jan 201712:22:54 02 Jan 20176 minutes 25 seconds
Preprocessing alignments for candidate junction identification12:22:54 02 Jan 201712:24:10 02 Jan 20171 minute 16 seconds
Preliminary analysis of coverage distribution12:24:10 02 Jan 201712:26:24 02 Jan 20172 minutes 14 seconds
Identifying junction candidates12:26:24 02 Jan 201712:26:25 02 Jan 20171 second
Re-alignment to junction candidates12:26:25 02 Jan 201712:27:49 02 Jan 20171 minute 24 seconds
Resolving alignments with junction candidates12:27:49 02 Jan 201712:29:58 02 Jan 20172 minutes 9 seconds
Creating BAM files12:29:58 02 Jan 201712:31:36 02 Jan 20171 minute 38 seconds
Tabulating error counts12:31:36 02 Jan 201712:33:26 02 Jan 20171 minute 50 seconds
Re-calibrating base error rates12:33:26 02 Jan 201712:33:27 02 Jan 20171 second
Examining read alignment evidence12:33:27 02 Jan 201712:48:31 02 Jan 201715 minutes 4 seconds
Polymorphism statistics12:48:31 02 Jan 201712:48:32 02 Jan 20171 second
Output12:48:32 02 Jan 201712:48:48 02 Jan 201716 seconds
Total 33 minutes 6 seconds