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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsGlu_KHP_A10_F418_I3_R1_S20_L008_R1_001.good.fq4,354,560431,101,440100.0%99.0 bases99 bases96.4%
errorsGlu_KHP_A10_F418_I3_R1_S20_L008_R2_001.good.fq4,276,456423,369,144100.0%99.0 bases99 bases93.3%
total8,631,016854,470,584100.0%99.0 bases99 bases94.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652172.02.4100.0%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≤ 100000100033
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 ≤ 5000715
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.032

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.49761

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 input11:16:07 23 May 201911:17:36 23 May 20191 minute 29 seconds
Read alignment to reference genome11:17:37 23 May 201911:32:16 23 May 201914 minutes 39 seconds
Preprocessing alignments for candidate junction identification11:32:16 23 May 201911:33:58 23 May 20191 minute 42 seconds
Preliminary analysis of coverage distribution11:33:58 23 May 201911:37:25 23 May 20193 minutes 27 seconds
Identifying junction candidates11:37:25 23 May 201911:39:50 23 May 20192 minutes 25 seconds
Re-alignment to junction candidates11:39:50 23 May 201911:44:32 23 May 20194 minutes 42 seconds
Resolving best read alignments11:44:32 23 May 201911:47:14 23 May 20192 minutes 42 seconds
Creating BAM files11:47:14 23 May 201911:50:18 23 May 20193 minutes 4 seconds
Tabulating error counts11:50:18 23 May 201911:51:31 23 May 20191 minute 13 seconds
Re-calibrating base error rates11:51:31 23 May 201911:51:32 23 May 20191 second
Examining read alignment evidence11:51:32 23 May 201912:04:27 23 May 201912 minutes 55 seconds
Polymorphism statistics12:04:27 23 May 201912:04:29 23 May 20192 seconds
Output12:04:29 23 May 201912:05:05 23 May 201936 seconds
Total 48 minutes 57 seconds