breseq  version 0.35.4  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsATCC_S10_L001_R1_001902,159194,754,06099.9%215.9 bases251 bases93.2%
total902,159194,754,06099.9%215.9 bases251 bases93.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistribution12,102,52491.36.2100.0%Aggregatibacter actinomycetemcomitans Aa31S
coveragedistribution2196NANA0.0%Aggregatibacter actinomycetemcomitans Aa31S
total2,102,720100.0%

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.

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

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 10000017168
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 ≤ 5000371
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.090

Junction Skew Score Calculation

reference sequencepr(no read start)
10.86331
2NA

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
bowtie22.4.1
R4.0.0

Execution Times

stepstartendelapsed
Read and reference sequence file input14:43:24 20 Jan 202214:43:42 20 Jan 202218 seconds
Read alignment to reference genome14:43:43 20 Jan 202214:44:34 20 Jan 202251 seconds
Preprocessing alignments for candidate junction identification14:44:34 20 Jan 202214:44:51 20 Jan 202217 seconds
Preliminary analysis of coverage distribution14:44:51 20 Jan 202214:45:34 20 Jan 202243 seconds
Identifying junction candidates14:45:34 20 Jan 202214:46:00 20 Jan 202226 seconds
Re-alignment to junction candidates14:46:00 20 Jan 202214:46:18 20 Jan 202218 seconds
Resolving best read alignments14:46:18 20 Jan 202214:46:44 20 Jan 202226 seconds
Creating BAM files14:46:44 20 Jan 202214:47:20 20 Jan 202236 seconds
Tabulating error counts14:47:20 20 Jan 202214:47:38 20 Jan 202218 seconds
Re-calibrating base error rates14:47:38 20 Jan 202214:47:39 20 Jan 20221 second
Examining read alignment evidence14:47:39 20 Jan 202214:51:15 20 Jan 20223 minutes 36 seconds
Polymorphism statistics14:51:15 20 Jan 202214:51:16 20 Jan 20221 second
Output14:51:16 20 Jan 202214:52:07 20 Jan 202251 seconds
Total 8 minutes 42 seconds