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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorspgi-2-3_S5_L001_R1_001.good.fq1,026,539220,161,511100.0%214.5 bases239 bases96.8%
errorspgi-2-3_S5_L001_R2_001.good.fq1,026,539223,047,760100.0%217.3 bases239 bases68.8%
total2,053,078443,209,271100.0%215.9 bases239 bases82.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65279.97.6100.0%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≤ 1000002546
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 ≤ 5000158
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.016

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.88376

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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input01:44:37 28 Feb 202001:45:06 28 Feb 202029 seconds
Read alignment to reference genome01:45:06 28 Feb 202001:55:46 28 Feb 202010 minutes 40 seconds
Preprocessing alignments for candidate junction identification01:55:46 28 Feb 202001:56:17 28 Feb 202031 seconds
Preliminary analysis of coverage distribution01:56:17 28 Feb 202001:57:45 28 Feb 20201 minute 28 seconds
Identifying junction candidates01:57:45 28 Feb 202001:57:48 28 Feb 20203 seconds
Re-alignment to junction candidates01:57:48 28 Feb 202001:59:53 28 Feb 20202 minutes 5 seconds
Resolving best read alignments01:59:53 28 Feb 202002:00:44 28 Feb 202051 seconds
Creating BAM files02:00:44 28 Feb 202002:02:04 28 Feb 20201 minute 20 seconds
Tabulating error counts02:02:04 28 Feb 202002:02:32 28 Feb 202028 seconds
Re-calibrating base error rates02:02:32 28 Feb 202002:02:33 28 Feb 20201 second
Examining read alignment evidence02:02:33 28 Feb 202002:41:04 28 Feb 202038 minutes 31 seconds
Polymorphism statistics02:41:04 28 Feb 202002:41:05 28 Feb 20201 second
Output02:41:05 28 Feb 202002:41:24 28 Feb 202019 seconds
Total 56 minutes 47 seconds