breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR2001828_R1.good.fq5,847,855290,065,246100.0%49.6 bases50 bases97.1%
errorsERR2001828_R2.good.fq5,847,853290,062,216100.0%49.6 bases50 bases96.6%
total11,695,708580,127,462100.0%49.6 bases50 bases96.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652166.116.4100.0%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≤ 10000012920
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 ≤ 5000231
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.48116

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 cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
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

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input01:54:01 03 Apr 201901:55:39 03 Apr 20191 minute 38 seconds
Read alignment to reference genome01:55:39 03 Apr 201902:58:29 03 Apr 20191 hour 2 minutes 50 seconds
Preprocessing alignments for candidate junction identification02:58:29 03 Apr 201903:00:11 03 Apr 20191 minute 42 seconds
Preliminary analysis of coverage distribution03:00:11 03 Apr 201903:03:30 03 Apr 20193 minutes 19 seconds
Identifying junction candidates03:03:30 03 Apr 201903:03:34 03 Apr 20194 seconds
Re-alignment to junction candidates03:03:34 03 Apr 201903:06:35 03 Apr 20193 minutes 1 second
Resolving best read alignments03:06:35 03 Apr 201903:09:17 03 Apr 20192 minutes 42 seconds
Creating BAM files03:09:17 03 Apr 201903:12:19 03 Apr 20193 minutes 2 seconds
Tabulating error counts03:12:19 03 Apr 201903:13:08 03 Apr 201949 seconds
Re-calibrating base error rates03:13:08 03 Apr 201903:13:09 03 Apr 20191 second
Examining read alignment evidence03:13:09 03 Apr 201903:20:55 03 Apr 20197 minutes 46 seconds
Polymorphism statistics03:20:55 03 Apr 201903:20:56 03 Apr 20191 second
Output03:20:56 03 Apr 201903:21:44 03 Apr 201948 seconds
Total 1 hour 27 minutes 43 seconds