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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsROS_KHP_18-36_CLONE_S60_L007_R1_001.good.fq5,576,342556,872,997100.0%99.9 bases100 bases98.1%
errorsROS_KHP_18-36_CLONE_S60_L007_R2_001.good.fq5,576,341495,842,510100.0%88.9 bases89 bases97.6%
total11,152,6831,052,715,507100.0%94.4 bases100 bases97.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652214.32.3100.0%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≤ 100000100000
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 ≤ 5000851
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.038

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.38744

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 input10:49:46 30 Mar 201910:51:52 30 Mar 20192 minutes 6 seconds
Read alignment to reference genome10:51:52 30 Mar 201911:08:55 30 Mar 201917 minutes 3 seconds
Preprocessing alignments for candidate junction identification11:08:55 30 Mar 201911:11:04 30 Mar 20192 minutes 9 seconds
Preliminary analysis of coverage distribution11:11:04 30 Mar 201911:15:13 30 Mar 20194 minutes 9 seconds
Identifying junction candidates11:15:13 30 Mar 201911:17:45 30 Mar 20192 minutes 32 seconds
Re-alignment to junction candidates11:17:45 30 Mar 201911:24:01 30 Mar 20196 minutes 16 seconds
Resolving best read alignments11:24:01 30 Mar 201911:27:40 30 Mar 20193 minutes 39 seconds
Creating BAM files11:27:40 30 Mar 201911:31:16 30 Mar 20193 minutes 36 seconds
Tabulating error counts11:31:16 30 Mar 201911:32:50 30 Mar 20191 minute 34 seconds
Re-calibrating base error rates11:32:50 30 Mar 201911:32:51 30 Mar 20191 second
Examining read alignment evidence11:32:51 30 Mar 201911:47:33 30 Mar 201914 minutes 42 seconds
Polymorphism statistics11:47:33 30 Mar 201911:47:34 30 Mar 20191 second
Output11:47:34 30 Mar 201911:48:28 30 Mar 201954 seconds
Total 58 minutes 42 seconds