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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJBEI_Xylose_A28_F48_I0_S29_R1_001.good.fq271,84236,193,677100.0%133.1 bases136 bases86.6%
errorsJBEI_Xylose_A28_F48_I0_S29_R2_001.good.fq271,84236,193,677100.0%133.1 bases136 bases74.0%
total543,68472,387,354100.0%133.1 bases136 bases80.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,183,8589.25.7100.0%na
total6,183,858100.0%

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≤ 100000910
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 ≤ 500052
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.97123

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 input23:30:21 17 Jul 202023:30:37 17 Jul 202016 seconds
Read alignment to reference genome23:30:38 17 Jul 202023:31:52 17 Jul 20201 minute 14 seconds
Preprocessing alignments for candidate junction identification23:31:52 17 Jul 202023:32:03 17 Jul 202011 seconds
Preliminary analysis of coverage distribution23:32:03 17 Jul 202023:32:20 17 Jul 202017 seconds
Identifying junction candidates23:32:20 17 Jul 202023:32:20 17 Jul 20200 seconds
Re-alignment to junction candidates23:32:20 17 Jul 202023:32:36 17 Jul 202016 seconds
Resolving best read alignments23:32:36 17 Jul 202023:32:55 17 Jul 202019 seconds
Creating BAM files23:32:55 17 Jul 202023:33:08 17 Jul 202013 seconds
Tabulating error counts23:33:08 17 Jul 202023:33:17 17 Jul 20209 seconds
Re-calibrating base error rates23:33:17 17 Jul 202023:33:18 17 Jul 20201 second
Examining read alignment evidence23:33:18 17 Jul 202023:36:21 17 Jul 20203 minutes 3 seconds
Polymorphism statistics23:36:21 17 Jul 202023:36:26 17 Jul 20205 seconds
Output23:36:26 17 Jul 202000:06:27 18 Jul 202030 minutes 1 second
Total 36 minutes 5 seconds