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_A25_F37_I1_S21_R1_001.good.fq3,208,066425,741,327100.0%132.7 bases136 bases96.7%
errorsJBEI_Xylose_A25_F37_I1_S21_R2_001.good.fq3,208,066425,741,327100.0%132.7 bases136 bases82.6%
total6,416,132851,482,654100.0%132.7 bases136 bases89.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,183,858134.58.0100.0%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≤ 10000010861
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 ≤ 5000557
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.025

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.77484

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≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
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 cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
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 ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input19:27:47 17 Jul 202019:30:33 17 Jul 20202 minutes 46 seconds
Read alignment to reference genome19:30:33 17 Jul 202019:47:30 17 Jul 202016 minutes 57 seconds
Preprocessing alignments for candidate junction identification19:47:30 17 Jul 202019:50:52 17 Jul 20203 minutes 22 seconds
Preliminary analysis of coverage distribution19:50:52 17 Jul 202019:54:59 17 Jul 20204 minutes 7 seconds
Identifying junction candidates19:54:59 17 Jul 202019:55:11 17 Jul 202012 seconds
Re-alignment to junction candidates19:55:11 17 Jul 202019:59:34 17 Jul 20204 minutes 23 seconds
Resolving best read alignments19:59:34 17 Jul 202020:07:23 17 Jul 20207 minutes 49 seconds
Creating BAM files20:07:23 17 Jul 202020:12:27 17 Jul 20205 minutes 4 seconds
Tabulating error counts20:12:27 17 Jul 202020:14:26 17 Jul 20201 minute 59 seconds
Re-calibrating base error rates20:14:26 17 Jul 202020:14:28 17 Jul 20202 seconds
Examining read alignment evidence20:14:28 17 Jul 202020:32:28 17 Jul 202018 minutes 0 seconds
Polymorphism statistics20:32:28 17 Jul 202020:32:29 17 Jul 20201 second
Output20:32:29 17 Jul 202020:33:06 17 Jul 202037 seconds
Total 1 hour 5 minutes 19 seconds