breseq  version 0.37.1  revision d7ab7d0ba1c1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsN_5_22_A11_S255_R1_0011,963,089289,811,463100.0%147.6 bases151 bases92.7%
errorsN_5_22_A11_S255_R2_0011,962,408289,635,782100.0%147.6 bases151 bases91.4%
total3,925,497579,447,245100.0%147.6 bases151 bases92.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionExported2,155,007248.63.7100.0%Neisseria gonorrhoeae strain N-1-60.
total2,155,007100.0%

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≤ 10000018111
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000425
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.064

Junction Skew Score Calculation

reference sequencepr(no read start)
Exported0.75724

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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 cutoff0.8
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
bowtie22.4.5
R4.2.2

Execution Times

stepstartendelapsed
Read and reference sequence file input22:37:07 02 Mar 202322:40:10 02 Mar 20233 minutes 3 seconds
Read alignment to reference genome22:40:11 02 Mar 202322:41:38 02 Mar 20231 minute 27 seconds
Preprocessing alignments for candidate junction identification22:41:38 02 Mar 202322:42:28 02 Mar 202350 seconds
Preliminary analysis of coverage distribution22:42:28 02 Mar 202322:43:40 02 Mar 20231 minute 12 seconds
Identifying junction candidates22:43:40 02 Mar 202322:45:08 02 Mar 20231 minute 28 seconds
Re-alignment to junction candidates22:45:08 02 Mar 202322:45:40 02 Mar 202332 seconds
Resolving best read alignments22:45:40 02 Mar 202322:46:49 02 Mar 20231 minute 9 seconds
Creating BAM files22:46:49 02 Mar 202322:47:47 02 Mar 202358 seconds
Tabulating error counts22:47:47 02 Mar 202322:48:39 02 Mar 202352 seconds
Re-calibrating base error rates22:48:39 02 Mar 202322:48:41 02 Mar 20232 seconds
Examining read alignment evidence22:48:41 02 Mar 202322:54:22 02 Mar 20235 minutes 41 seconds
Polymorphism statistics22:54:22 02 Mar 202322:54:22 02 Mar 20230 seconds
Output22:54:22 02 Mar 202322:54:31 02 Mar 20239 seconds
Output :: Mutation Prediction22:54:22 02 Mar 202322:54:23 02 Mar 20231 second
Output :: Mutation Annotation22:54:23 02 Mar 202322:54:23 02 Mar 20230 seconds
Total 17 minutes 24 seconds