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-8-91-2-1_S5_L001_R2_001688,663198,596,131100.0%288.4 bases301 bases83.6%
errorsSSW-KHP-SSW-8-91-2-1_S5_L001_R1_001688,859196,249,911100.0%284.9 bases301 bases95.7%
total1,377,522394,846,042100.0%286.6 bases301 bases89.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65274.12.4100.0%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≤ 1000009975
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 ≤ 500052
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.90417

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 input17:31:36 16 Mar 201617:32:32 16 Mar 201656 seconds
Read alignment to reference genome17:32:32 16 Mar 201617:36:29 16 Mar 20163 minutes 57 seconds
Preprocessing alignments for candidate junction identification17:36:29 16 Mar 201617:37:20 16 Mar 201651 seconds
Preliminary analysis of coverage distribution17:37:20 16 Mar 201617:40:22 16 Mar 20163 minutes 2 seconds
Identifying junction candidates17:40:22 16 Mar 201617:40:26 16 Mar 20164 seconds
Re-alignment to junction candidates17:40:26 16 Mar 201617:41:06 16 Mar 201640 seconds
Resolving alignments with junction candidates17:41:06 16 Mar 201617:43:06 16 Mar 20162 minutes 0 seconds
Creating BAM files17:43:06 16 Mar 201617:44:20 16 Mar 20161 minute 14 seconds
Tabulating error counts17:44:20 16 Mar 201617:46:42 16 Mar 20162 minutes 22 seconds
Re-calibrating base error rates17:46:42 16 Mar 201617:46:43 16 Mar 20161 second
Examining read alignment evidence17:46:43 16 Mar 201618:05:15 16 Mar 201618 minutes 32 seconds
Polymorphism statistics18:05:15 16 Mar 201618:05:16 16 Mar 20161 second
Output18:05:16 16 Mar 201618:05:49 16 Mar 201633 seconds
Total 34 minutes 13 seconds