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-GLUT1-9_S2_L001_R2_0011,105,873166,113,890100.0%150.2 bases151 bases97.3%
errorsqtrim-GLUT1-9_S2_L001_R1_0011,106,281166,464,974100.0%150.5 bases151 bases99.8%
total2,212,154332,578,864100.0%150.3 bases151 bases98.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65270.51.498.3%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≤ 1000001165
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 ≤ 500035
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_0009130.80292

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 input00:38:44 03 Jan 201700:39:15 03 Jan 201731 seconds
Read alignment to reference genome00:39:16 03 Jan 201700:43:30 03 Jan 20174 minutes 14 seconds
Preprocessing alignments for candidate junction identification00:43:30 03 Jan 201700:44:25 03 Jan 201755 seconds
Preliminary analysis of coverage distribution00:44:25 03 Jan 201700:46:06 03 Jan 20171 minute 41 seconds
Identifying junction candidates00:46:06 03 Jan 201700:46:07 03 Jan 20171 second
Re-alignment to junction candidates00:46:07 03 Jan 201700:47:04 03 Jan 201757 seconds
Resolving alignments with junction candidates00:47:04 03 Jan 201700:48:39 03 Jan 20171 minute 35 seconds
Creating BAM files00:48:39 03 Jan 201700:49:57 03 Jan 20171 minute 18 seconds
Tabulating error counts00:49:57 03 Jan 201700:51:25 03 Jan 20171 minute 28 seconds
Re-calibrating base error rates00:51:25 03 Jan 201700:51:25 03 Jan 20170 seconds
Examining read alignment evidence00:51:25 03 Jan 201701:02:41 03 Jan 201711 minutes 16 seconds
Polymorphism statistics01:02:41 03 Jan 201701:02:41 03 Jan 20170 seconds
Output01:02:41 03 Jan 201701:02:55 03 Jan 201714 seconds
Total 24 minutes 10 seconds