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-OCTA5-4_S10_L001_R1_0011,338,321201,036,344100.0%150.2 bases151 bases94.6%
errorsqtrim-OCTA5-4_S10_L001_R2_0011,339,040200,867,375100.0%150.0 bases151 bases93.4%
total2,677,361401,903,719100.0%150.1 bases151 bases94.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65281.71.398.3%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≤ 1000002813
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 ≤ 500020
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_0009130.77477

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 input14:20:06 02 Jan 201714:21:15 02 Jan 20171 minute 9 seconds
Read alignment to reference genome14:21:16 02 Jan 201714:29:52 02 Jan 20178 minutes 36 seconds
Preprocessing alignments for candidate junction identification14:29:52 02 Jan 201714:31:34 02 Jan 20171 minute 42 seconds
Preliminary analysis of coverage distribution14:31:34 02 Jan 201714:34:20 02 Jan 20172 minutes 46 seconds
Identifying junction candidates14:34:20 02 Jan 201714:34:21 02 Jan 20171 second
Re-alignment to junction candidates14:34:21 02 Jan 201714:36:04 02 Jan 20171 minute 43 seconds
Resolving alignments with junction candidates14:36:04 02 Jan 201714:38:35 02 Jan 20172 minutes 31 seconds
Creating BAM files14:38:35 02 Jan 201714:40:25 02 Jan 20171 minute 50 seconds
Tabulating error counts14:40:25 02 Jan 201714:42:36 02 Jan 20172 minutes 11 seconds
Re-calibrating base error rates14:42:36 02 Jan 201714:42:37 02 Jan 20171 second
Examining read alignment evidence14:42:37 02 Jan 201714:59:01 02 Jan 201716 minutes 24 seconds
Polymorphism statistics14:59:01 02 Jan 201714:59:02 02 Jan 20171 second
Output14:59:02 02 Jan 201714:59:25 02 Jan 201723 seconds
Total 39 minutes 18 seconds