breseq  version 0.32.0  revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsCCK_Evo02EP_Isolate_2_S1592_L005_R2_001.good.fq1,015,131143,262,073100.0%141.1 bases143 bases92.2%
errorsCCK_Evo02EP_Isolate_2_S1592_L005_R1_001.good.fq1,015,131143,262,073100.0%141.1 bases143 bases97.2%
total2,030,262286,524,146100.0%141.1 bases143 bases94.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65358.01.5100.0%Escherichia coli str. K-12 sbstr. MG1655, complete genome. Live strain from Systems Biology Research Group
total4,641,653100.0%

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≤ 10000012997
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 ≤ 5000647
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.042

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84410

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
bowtie22.2.8
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input17:04:10 17 Mar 201817:04:32 17 Mar 201822 seconds
Read alignment to reference genome17:04:32 17 Mar 201817:06:37 17 Mar 20182 minutes 5 seconds
Preprocessing alignments for candidate junction identification17:06:37 17 Mar 201817:07:22 17 Mar 201845 seconds
Preliminary analysis of coverage distribution17:07:22 17 Mar 201817:08:20 17 Mar 201858 seconds
Identifying junction candidates17:08:20 17 Mar 201817:08:28 17 Mar 20188 seconds
Re-alignment to junction candidates17:08:28 17 Mar 201817:08:50 17 Mar 201822 seconds
Resolving best read alignments17:08:50 17 Mar 201817:09:36 17 Mar 201846 seconds
Creating BAM files17:09:36 17 Mar 201817:10:26 17 Mar 201850 seconds
Tabulating error counts17:10:26 17 Mar 201817:10:49 17 Mar 201823 seconds
Re-calibrating base error rates17:10:49 17 Mar 201817:10:50 17 Mar 20181 second
Examining read alignment evidence17:10:50 17 Mar 201817:15:51 17 Mar 20185 minutes 1 second
Polymorphism statistics17:15:51 17 Mar 201817:15:51 17 Mar 20180 seconds
Output17:15:51 17 Mar 201817:16:02 17 Mar 201811 seconds
Total 11 minutes 52 seconds