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-3-164-6-1_S16_L001_R2_001234,20270,327,38999.9%300.3 bases301 bases73.9%
errorsSSW-KHP-SSW-3-164-6-1_S16_L001_R1_001234,51670,485,453100.0%300.6 bases301 bases76.3%
errorsSSW-KHP-SSW-3-164-6-1_S18_L001_R2_0011,728,625486,972,172100.0%281.7 bases301 bases93.5%
errorsSSW-KHP-SSW-3-164-6-1_S18_L001_R1_0011,728,714483,717,641100.0%279.8 bases301 bases98.0%
total3,926,0571,111,502,655100.0%283.1 bases301 bases93.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652221.82.6100.0%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≤ 10000012852
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 ≤ 500049
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_0009130.72335

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 input08:54:40 22 Mar 201608:56:32 22 Mar 20161 minute 52 seconds
Read alignment to reference genome08:56:32 22 Mar 201609:03:36 22 Mar 20167 minutes 4 seconds
Preprocessing alignments for candidate junction identification09:03:36 22 Mar 201609:05:34 22 Mar 20161 minute 58 seconds
Preliminary analysis of coverage distribution09:05:34 22 Mar 201609:11:09 22 Mar 20165 minutes 35 seconds
Identifying junction candidates09:11:09 22 Mar 201609:11:11 22 Mar 20162 seconds
Re-alignment to junction candidates09:11:11 22 Mar 201609:12:05 22 Mar 201654 seconds
Resolving alignments with junction candidates09:12:05 22 Mar 201609:17:21 22 Mar 20165 minutes 16 seconds
Creating BAM files09:17:21 22 Mar 201609:20:41 22 Mar 20163 minutes 20 seconds
Tabulating error counts09:20:41 22 Mar 201609:26:22 22 Mar 20165 minutes 41 seconds
Re-calibrating base error rates09:26:22 22 Mar 201609:26:23 22 Mar 20161 second
Examining read alignment evidence09:26:23 22 Mar 201610:07:08 22 Mar 201640 minutes 45 seconds
Polymorphism statistics10:07:08 22 Mar 201610:07:09 22 Mar 20161 second
Output10:07:09 22 Mar 201610:08:01 22 Mar 201652 seconds
Total 1 hour 13 minutes 21 seconds