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-GLUT5-9-rerun_S16_L001_R2_0011,036,601155,788,541100.0%150.3 bases151 bases98.3%
errorsqtrim-GLUT5-9-rerun_S16_L001_R1_0011,036,980156,026,769100.0%150.5 bases151 bases99.7%
total2,073,581311,815,310100.0%150.4 bases151 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65266.61.498.3%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≤ 100000964
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 ≤ 500032
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81030

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 input18:52:48 02 Jan 201718:53:18 02 Jan 201730 seconds
Read alignment to reference genome18:53:19 02 Jan 201718:57:13 02 Jan 20173 minutes 54 seconds
Preprocessing alignments for candidate junction identification18:57:13 02 Jan 201718:58:06 02 Jan 201753 seconds
Preliminary analysis of coverage distribution18:58:06 02 Jan 201718:59:42 02 Jan 20171 minute 36 seconds
Identifying junction candidates18:59:42 02 Jan 201718:59:42 02 Jan 20170 seconds
Re-alignment to junction candidates18:59:42 02 Jan 201719:00:35 02 Jan 201753 seconds
Resolving alignments with junction candidates19:00:35 02 Jan 201719:02:06 02 Jan 20171 minute 31 seconds
Creating BAM files19:02:06 02 Jan 201719:03:21 02 Jan 20171 minute 15 seconds
Tabulating error counts19:03:21 02 Jan 201719:04:43 02 Jan 20171 minute 22 seconds
Re-calibrating base error rates19:04:43 02 Jan 201719:04:44 02 Jan 20171 second
Examining read alignment evidence19:04:44 02 Jan 201719:15:22 02 Jan 201710 minutes 38 seconds
Polymorphism statistics19:15:22 02 Jan 201719:15:22 02 Jan 20170 seconds
Output19:15:22 02 Jan 201719:15:36 02 Jan 201714 seconds
Total 22 minutes 47 seconds