breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-KHP-SSW-2-165-1-1_S9_L001_R2_0011,645,841494,165,38799.9%300.3 bases301 bases81.9%
errorsSSW-KHP-SSW-2-165-1-1_S9_L001_R1_0011,647,900495,302,421100.0%300.6 bases301 bases84.9%
total3,293,741989,467,80899.9%300.4 bases301 bases83.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652176.52.0100.0%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≤ 10000011748
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500072
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.010

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.79595

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 input19:36:13 05 Mar 201619:37:52 05 Mar 20161 minute 39 seconds
Read alignment to reference genome19:37:53 05 Mar 201619:46:26 05 Mar 20168 minutes 33 seconds
Preprocessing alignments for candidate junction identification19:46:26 05 Mar 201619:48:07 05 Mar 20161 minute 41 seconds
Preliminary analysis of coverage distribution19:48:07 05 Mar 201619:52:35 05 Mar 20164 minutes 28 seconds
Identifying junction candidates19:52:35 05 Mar 201619:52:38 05 Mar 20163 seconds
Re-alignment to junction candidates19:52:38 05 Mar 201619:53:30 05 Mar 201652 seconds
Resolving alignments with junction candidates19:53:30 05 Mar 201619:58:04 05 Mar 20164 minutes 34 seconds
Creating BAM files19:58:04 05 Mar 201620:00:53 05 Mar 20162 minutes 49 seconds
Tabulating error counts20:00:53 05 Mar 201620:05:30 05 Mar 20164 minutes 37 seconds
Re-calibrating base error rates20:05:30 05 Mar 201620:05:31 05 Mar 20161 second
Examining read alignment evidence20:05:31 05 Mar 201620:38:46 05 Mar 201633 minutes 15 seconds
Polymorphism statistics20:38:46 05 Mar 201620:38:47 05 Mar 20161 second
Output20:38:47 05 Mar 201620:39:31 05 Mar 201644 seconds
Total 1 hour 3 minutes 17 seconds