breseq  version 0.35.7  revision b7a44cd89118
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsG2_CCGTCC_L007_R1_001503,25763,410,382100.0%126.0 bases126 bases98.1%
errorsG2_CCGTCC_L007_R2_001502,54463,320,54499.9%126.0 bases126 bases97.9%
total1,005,801126,730,92699.9%126.0 bases126 bases98.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionADP1-WT3,600,835NANA100.0%Acinetobacter sp. ADP1 chromosome, complete genome.

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.

Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing or the -c,--contig-reference option if you want mutations called for these reference sequences.

New Junction Evidence

Junction Candidates Tested

Number of alignment pairs examined for constructing junction candidates≤ 100000336
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 ≤ 500014
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)

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

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

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


Execution Times

Read and reference sequence file input10:38:31 20 Jul 202110:39:08 20 Jul 202137 seconds
Read alignment to reference genome10:39:08 20 Jul 202110:39:50 20 Jul 202142 seconds
Preprocessing alignments for candidate junction identification10:39:50 20 Jul 202110:40:13 20 Jul 202123 seconds
Preliminary analysis of coverage distribution10:40:13 20 Jul 202110:40:34 20 Jul 202121 seconds
Identifying junction candidates10:40:34 20 Jul 202110:40:34 20 Jul 20210 seconds
Re-alignment to junction candidates10:40:34 20 Jul 202110:40:43 20 Jul 20219 seconds
Resolving best read alignments10:40:43 20 Jul 202110:41:20 20 Jul 202137 seconds
Creating BAM files10:41:20 20 Jul 202110:41:36 20 Jul 202116 seconds
Tabulating error counts10:41:36 20 Jul 202110:41:47 20 Jul 202111 seconds
Re-calibrating base error rates10:41:47 20 Jul 202110:41:47 20 Jul 20210 seconds
Examining read alignment evidence10:41:47 20 Jul 202110:42:53 20 Jul 20211 minute 6 seconds
Polymorphism statistics10:42:53 20 Jul 202110:42:54 20 Jul 20211 second
Output10:42:54 20 Jul 202110:42:56 20 Jul 20212 seconds
Output :: Mutation Prediction10:42:54 20 Jul 202110:42:54 20 Jul 20210 seconds
Output :: Mutation Annotation10:42:54 20 Jul 202110:42:54 20 Jul 20210 seconds
Total 4 minutes 25 seconds