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_A27_F51_I0_S25_R1_001.good.fq569,52775,866,894100.0%133.2 bases136 bases85.6%
errorsJBEI_Xylose_A27_F51_I0_S25_R2_001.good.fq569,52775,866,894100.0%133.2 bases136 bases73.2%
total1,139,054151,733,788100.0%133.2 bases136 bases79.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,183,85821.18.0100.0%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≤ 1000001388
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 ≤ 500056
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_0029470.94493

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 input21:06:12 17 Jul 202021:06:42 17 Jul 202030 seconds
Read alignment to reference genome21:06:43 17 Jul 202021:09:15 17 Jul 20202 minutes 32 seconds
Preprocessing alignments for candidate junction identification21:09:15 17 Jul 202021:09:39 17 Jul 202024 seconds
Preliminary analysis of coverage distribution21:09:39 17 Jul 202021:10:12 17 Jul 202033 seconds
Identifying junction candidates21:10:12 17 Jul 202021:10:12 17 Jul 20200 seconds
Re-alignment to junction candidates21:10:12 17 Jul 202021:10:46 17 Jul 202034 seconds
Resolving best read alignments21:10:46 17 Jul 202021:11:26 17 Jul 202040 seconds
Creating BAM files21:11:26 17 Jul 202021:11:54 17 Jul 202028 seconds
Tabulating error counts21:11:54 17 Jul 202021:12:12 17 Jul 202018 seconds
Re-calibrating base error rates21:12:12 17 Jul 202021:12:14 17 Jul 20202 seconds
Examining read alignment evidence21:12:14 17 Jul 202021:17:46 17 Jul 20205 minutes 32 seconds
Polymorphism statistics21:17:46 17 Jul 202021:17:48 17 Jul 20202 seconds
Output21:17:48 17 Jul 202021:23:09 17 Jul 20205 minutes 21 seconds
Total 16 minutes 56 seconds