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-3-164-5-1_S15_L001_R1_001197,91859,489,519100.0%300.6 bases301 bases70.0%
errorsSSW-KHP-SSW-3-164-5-1_S15_L001_R2_001197,64259,356,89499.9%300.3 bases301 bases68.0%
errorsSSW-KHP-SSW-3-164-5-1_S3_L001_R2_001469,419128,551,050100.0%273.9 bases301 bases95.0%
errorsSSW-KHP-SSW-3-164-5-1_S3_L001_R1_001469,430127,897,746100.0%272.5 bases301 bases97.8%
total1,334,409375,295,209100.0%281.2 bases301 bases88.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65270.42.0100.0%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≤ 1000006942
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 ≤ 500028
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.004

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.89552

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 input14:00:01 21 Mar 201614:00:41 21 Mar 201640 seconds
Read alignment to reference genome14:00:41 21 Mar 201614:03:20 21 Mar 20162 minutes 39 seconds
Preprocessing alignments for candidate junction identification14:03:20 21 Mar 201614:04:02 21 Mar 201642 seconds
Preliminary analysis of coverage distribution14:04:02 21 Mar 201614:05:47 21 Mar 20161 minute 45 seconds
Identifying junction candidates14:05:47 21 Mar 201614:05:48 21 Mar 20161 second
Re-alignment to junction candidates14:05:48 21 Mar 201614:06:06 21 Mar 201618 seconds
Resolving alignments with junction candidates14:06:06 21 Mar 201614:07:31 21 Mar 20161 minute 25 seconds
Creating BAM files14:07:31 21 Mar 201614:08:33 21 Mar 20161 minute 2 seconds
Tabulating error counts14:08:33 21 Mar 201614:10:23 21 Mar 20161 minute 50 seconds
Re-calibrating base error rates14:10:23 21 Mar 201614:10:24 21 Mar 20161 second
Examining read alignment evidence14:10:24 21 Mar 201614:23:20 21 Mar 201612 minutes 56 seconds
Polymorphism statistics14:23:20 21 Mar 201614:23:21 21 Mar 20161 second
Output14:23:21 21 Mar 201614:23:45 21 Mar 201624 seconds
Total 23 minutes 44 seconds