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-GLUT4-4-rerun_S15_L001_R1_0011,056,724159,006,220100.0%150.5 bases151 bases99.8%
errorsqtrim-GLUT4-4-rerun_S15_L001_R2_0011,056,064158,467,38499.9%150.1 bases151 bases95.6%
total2,112,788317,473,604100.0%150.3 bases151 bases97.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65266.81.398.3%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≤ 1000001239
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_0009130.81053

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 input14:33:30 02 Jan 201714:34:13 02 Jan 201743 seconds
Read alignment to reference genome14:34:14 02 Jan 201714:41:20 02 Jan 20177 minutes 6 seconds
Preprocessing alignments for candidate junction identification14:41:20 02 Jan 201714:42:37 02 Jan 20171 minute 17 seconds
Preliminary analysis of coverage distribution14:42:37 02 Jan 201714:44:30 02 Jan 20171 minute 53 seconds
Identifying junction candidates14:44:30 02 Jan 201714:44:31 02 Jan 20171 second
Re-alignment to junction candidates14:44:31 02 Jan 201714:45:57 02 Jan 20171 minute 26 seconds
Resolving alignments with junction candidates14:45:57 02 Jan 201714:48:01 02 Jan 20172 minutes 4 seconds
Creating BAM files14:48:01 02 Jan 201714:49:25 02 Jan 20171 minute 24 seconds
Tabulating error counts14:49:25 02 Jan 201714:51:03 02 Jan 20171 minute 38 seconds
Re-calibrating base error rates14:51:03 02 Jan 201714:51:04 02 Jan 20171 second
Examining read alignment evidence14:51:04 02 Jan 201715:04:26 02 Jan 201713 minutes 22 seconds
Polymorphism statistics15:04:26 02 Jan 201715:04:26 02 Jan 20170 seconds
Output15:04:26 02 Jan 201715:04:43 02 Jan 201717 seconds
Total 31 minutes 12 seconds