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_F58_I2_S15_R1_001.good.fq4,727,832627,939,005100.0%132.8 bases136 bases97.1%
errorsJBEI_Xylose_A27_F58_I2_S15_R2_001.good.fq4,727,832627,939,005100.0%132.8 bases136 bases83.0%
total9,455,6641,255,878,010100.0%132.8 bases136 bases90.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,183,858214.635.2100.0%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≤ 10000012329
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 ≤ 5000589
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.027

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.73125

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 input21:49:43 17 Jul 202021:53:39 17 Jul 20203 minutes 56 seconds
Read alignment to reference genome21:53:40 17 Jul 202022:16:55 17 Jul 202023 minutes 15 seconds
Preprocessing alignments for candidate junction identification22:16:55 17 Jul 202022:21:28 17 Jul 20204 minutes 33 seconds
Preliminary analysis of coverage distribution22:21:28 17 Jul 202022:27:10 17 Jul 20205 minutes 42 seconds
Identifying junction candidates22:27:10 17 Jul 202022:27:18 17 Jul 20208 seconds
Re-alignment to junction candidates22:27:18 17 Jul 202022:33:10 17 Jul 20205 minutes 52 seconds
Resolving best read alignments22:33:10 17 Jul 202022:40:16 17 Jul 20207 minutes 6 seconds
Creating BAM files22:40:16 17 Jul 202022:44:57 17 Jul 20204 minutes 41 seconds
Tabulating error counts22:44:57 17 Jul 202022:47:53 17 Jul 20202 minutes 56 seconds
Re-calibrating base error rates22:47:53 17 Jul 202022:47:55 17 Jul 20202 seconds
Examining read alignment evidence22:47:55 17 Jul 202023:13:37 17 Jul 202025 minutes 42 seconds
Polymorphism statistics23:13:37 17 Jul 202023:13:39 17 Jul 20202 seconds
Output23:13:39 17 Jul 202023:14:23 17 Jul 202044 seconds
Total 1 hour 24 minutes 39 seconds