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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsGlyD_D40_I0_S2128_L001_R1_001.good.fq1,298,833193,474,836100.0%149.0 bases149 bases98.4%
errorsGlyD_D40_I0_S2128_L001_R2_001.good.fq1,298,833193,474,836100.0%149.0 bases149 bases92.6%
total2,597,666386,949,672100.0%149.0 bases149 bases95.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65378.56.9100.0%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≤ 1000006488
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 ≤ 500042
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81487

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 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 cutoff2
Polymorphism frequency cutoff0.05
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
bowtie22.3.4.3
R3.5.1

Execution Times

stepstartendelapsed
Read and reference sequence file input04:47:06 30 Oct 201804:47:41 30 Oct 201835 seconds
Read alignment to reference genome04:47:42 30 Oct 201804:54:06 30 Oct 20186 minutes 24 seconds
Preprocessing alignments for candidate junction identification04:54:06 30 Oct 201804:54:36 30 Oct 201830 seconds
Preliminary analysis of coverage distribution04:54:36 30 Oct 201804:56:17 30 Oct 20181 minute 41 seconds
Identifying junction candidates04:56:17 30 Oct 201804:56:17 30 Oct 20180 seconds
Re-alignment to junction candidates04:56:17 30 Oct 201804:57:27 30 Oct 20181 minute 10 seconds
Resolving best read alignments04:57:27 30 Oct 201804:58:19 30 Oct 201852 seconds
Creating BAM files04:58:19 30 Oct 201804:59:52 30 Oct 20181 minute 33 seconds
Tabulating error counts04:59:52 30 Oct 201805:00:21 30 Oct 201829 seconds
Re-calibrating base error rates05:00:21 30 Oct 201805:00:22 30 Oct 20181 second
Examining read alignment evidence05:00:22 30 Oct 201805:38:04 30 Oct 201837 minutes 42 seconds
Polymorphism statistics05:38:04 30 Oct 201805:38:04 30 Oct 20180 seconds
Output05:38:04 30 Oct 201805:38:13 30 Oct 20189 seconds
Total 51 minutes 6 seconds