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-HEXA1-5_S3_L001_R2_0011,252,061188,279,532100.0%150.4 bases151 bases99.1%
errorsqtrim-HEXA1-5_S3_L001_R1_0011,252,068188,370,579100.0%150.4 bases151 bases99.8%
total2,504,129376,650,111100.0%150.4 bases151 bases99.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65280.81.298.3%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≤ 100000447
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 ≤ 500018
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_0009130.77549

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 input14:46:40 02 Jan 201714:47:35 02 Jan 201755 seconds
Read alignment to reference genome14:47:36 02 Jan 201714:54:49 02 Jan 20177 minutes 13 seconds
Preprocessing alignments for candidate junction identification14:54:49 02 Jan 201714:56:15 02 Jan 20171 minute 26 seconds
Preliminary analysis of coverage distribution14:56:15 02 Jan 201714:58:42 02 Jan 20172 minutes 27 seconds
Identifying junction candidates14:58:42 02 Jan 201714:58:42 02 Jan 20170 seconds
Re-alignment to junction candidates14:58:42 02 Jan 201715:00:12 02 Jan 20171 minute 30 seconds
Resolving alignments with junction candidates15:00:12 02 Jan 201715:02:25 02 Jan 20172 minutes 13 seconds
Creating BAM files15:02:25 02 Jan 201715:04:07 02 Jan 20171 minute 42 seconds
Tabulating error counts15:04:07 02 Jan 201715:06:05 02 Jan 20171 minute 58 seconds
Re-calibrating base error rates15:06:05 02 Jan 201715:06:06 02 Jan 20171 second
Examining read alignment evidence15:06:06 02 Jan 201715:21:42 02 Jan 201715 minutes 36 seconds
Polymorphism statistics15:21:42 02 Jan 201715:21:43 02 Jan 20171 second
Output15:21:43 02 Jan 201715:22:01 02 Jan 201718 seconds
Total 35 minutes 20 seconds