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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALEevo04-ptsHIcrr-kan_S5_L001_R1_001.good.fq532,583135,155,455100.0%253.8 bases275 bases98.2%
errorsALEevo04-ptsHIcrr-kan_S5_L001_R2_001.good.fq532,582134,757,019100.0%253.0 bases275 bases97.3%
total1,065,165269,912,474100.0%253.4 bases275 bases97.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65356.83.4100.0%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≤ 1000005664
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 ≤ 5000534
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.064

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.91844

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 input14:06:14 18 Mar 201814:06:30 18 Mar 201816 seconds
Read alignment to reference genome14:06:30 18 Mar 201814:08:47 18 Mar 20182 minutes 17 seconds
Preprocessing alignments for candidate junction identification14:08:47 18 Mar 201814:09:06 18 Mar 201819 seconds
Preliminary analysis of coverage distribution14:09:06 18 Mar 201814:09:53 18 Mar 201847 seconds
Identifying junction candidates14:09:53 18 Mar 201814:10:02 18 Mar 20189 seconds
Re-alignment to junction candidates14:10:02 18 Mar 201814:10:27 18 Mar 201825 seconds
Resolving best read alignments14:10:27 18 Mar 201814:11:00 18 Mar 201833 seconds
Creating BAM files14:11:00 18 Mar 201814:11:39 18 Mar 201839 seconds
Tabulating error counts14:11:39 18 Mar 201814:12:04 18 Mar 201825 seconds
Re-calibrating base error rates14:12:04 18 Mar 201814:12:04 18 Mar 20180 seconds
Examining read alignment evidence14:12:04 18 Mar 201814:44:26 18 Mar 201832 minutes 22 seconds
Polymorphism statistics14:44:26 18 Mar 201814:44:27 18 Mar 20181 second
Output14:44:27 18 Mar 201814:44:39 18 Mar 201812 seconds
Total 38 minutes 25 seconds