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_A9_F433_I3_R1_S34_L008_R1_001.good.fq4,138,682409,729,518100.0%99.0 bases99 bases95.2%
errorsGlu_KHP_A9_F433_I3_R1_S34_L008_R2_001.good.fq4,060,984402,037,416100.0%99.0 bases99 bases92.0%
total8,199,666811,766,934100.0%99.0 bases99 bases93.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652161.12.8100.0%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≤ 100000100026
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 ≤ 50001245
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.055

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.51804

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 input20:10:22 22 May 201920:11:47 22 May 20191 minute 25 seconds
Read alignment to reference genome20:11:47 22 May 201920:26:05 22 May 201914 minutes 18 seconds
Preprocessing alignments for candidate junction identification20:26:05 22 May 201920:27:43 22 May 20191 minute 38 seconds
Preliminary analysis of coverage distribution20:27:43 22 May 201920:30:58 22 May 20193 minutes 15 seconds
Identifying junction candidates20:30:58 22 May 201920:36:47 22 May 20195 minutes 49 seconds
Re-alignment to junction candidates20:36:47 22 May 201920:41:43 22 May 20194 minutes 56 seconds
Resolving best read alignments20:41:43 22 May 201920:44:17 22 May 20192 minutes 34 seconds
Creating BAM files20:44:17 22 May 201920:47:18 22 May 20193 minutes 1 second
Tabulating error counts20:47:18 22 May 201920:48:26 22 May 20191 minute 8 seconds
Re-calibrating base error rates20:48:26 22 May 201920:48:27 22 May 20191 second
Examining read alignment evidence20:48:27 22 May 201920:59:59 22 May 201911 minutes 32 seconds
Polymorphism statistics20:59:59 22 May 201921:00:01 22 May 20192 seconds
Output21:00:01 22 May 201921:00:52 22 May 201951 seconds
Total 50 minutes 30 seconds