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_B5_S257_R1_0011,693,776249,710,038100.0%147.4 bases151 bases89.7%
errorsN_5_22_B5_S257_R2_0011,693,187249,536,125100.0%147.4 bases151 bases88.8%
total3,386,963499,246,163100.0%147.4 bases151 bases89.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionExported2,155,007208.03.4100.0%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≤ 10000012309
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 ≤ 5000350
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.052

Junction Skew Score Calculation

reference sequencepr(no read start)
Exported0.77495

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 input23:10:33 02 Mar 202323:11:29 02 Mar 202356 seconds
Read alignment to reference genome23:11:29 02 Mar 202323:12:35 02 Mar 20231 minute 6 seconds
Preprocessing alignments for candidate junction identification23:12:35 02 Mar 202323:13:12 02 Mar 202337 seconds
Preliminary analysis of coverage distribution23:13:12 02 Mar 202323:14:13 02 Mar 20231 minute 1 second
Identifying junction candidates23:14:13 02 Mar 202323:15:13 02 Mar 20231 minute 0 seconds
Re-alignment to junction candidates23:15:13 02 Mar 202323:15:39 02 Mar 202326 seconds
Resolving best read alignments23:15:39 02 Mar 202323:16:37 02 Mar 202358 seconds
Creating BAM files23:16:37 02 Mar 202323:17:29 02 Mar 202352 seconds
Tabulating error counts23:17:29 02 Mar 202323:18:13 02 Mar 202344 seconds
Re-calibrating base error rates23:18:13 02 Mar 202323:18:14 02 Mar 20231 second
Examining read alignment evidence23:18:14 02 Mar 202323:22:50 02 Mar 20234 minutes 36 seconds
Polymorphism statistics23:22:50 02 Mar 202323:22:51 02 Mar 20231 second
Output23:22:51 02 Mar 202323:22:58 02 Mar 20237 seconds
Output :: Mutation Prediction23:22:51 02 Mar 202323:22:52 02 Mar 20231 second
Output :: Mutation Annotation23:22:52 02 Mar 202323:22:52 02 Mar 20230 seconds
Total 12 minutes 26 seconds