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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorspgi-7-1_S8_L001_R2_001.good.fq1,232,609283,908,841100.0%230.3 bases239 bases95.3%
errorspgi-7-1_S8_L001_R1_001.good.fq1,232,609283,671,316100.0%230.1 bases239 bases99.8%
total2,465,218567,580,157100.0%230.2 bases239 bases97.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,653124.75.8100.0%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≤ 1000005367
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 ≤ 5000241
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.025

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84295

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoffOFF
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.025
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.2.8
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input06:23:58 19 Mar 201806:24:32 19 Mar 201834 seconds
Read alignment to reference genome06:24:33 19 Mar 201806:27:03 19 Mar 20182 minutes 30 seconds
Preprocessing alignments for candidate junction identification06:27:03 19 Mar 201806:27:43 19 Mar 201840 seconds
Preliminary analysis of coverage distribution06:27:43 19 Mar 201806:29:17 19 Mar 20181 minute 34 seconds
Identifying junction candidates06:29:17 19 Mar 201806:29:21 19 Mar 20184 seconds
Re-alignment to junction candidates06:29:21 19 Mar 201806:29:53 19 Mar 201832 seconds
Resolving best read alignments06:29:53 19 Mar 201806:31:04 19 Mar 20181 minute 11 seconds
Creating BAM files06:31:04 19 Mar 201806:32:23 19 Mar 20181 minute 19 seconds
Tabulating error counts06:32:23 19 Mar 201806:33:07 19 Mar 201844 seconds
Re-calibrating base error rates06:33:07 19 Mar 201806:33:08 19 Mar 20181 second
Examining read alignment evidence06:33:08 19 Mar 201807:20:54 19 Mar 201847 minutes 46 seconds
Polymorphism statistics07:20:54 19 Mar 201807:20:56 19 Mar 20182 seconds
Output07:20:56 19 Mar 201807:21:22 19 Mar 201826 seconds
Total 57 minutes 23 seconds