breseq  version 0.32.0  revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorseTMglc2_S2_L001_R2_001.good.fq1,221,803276,058,140100.0%225.9 bases240 bases96.8%
errorseTMglc2_S2_L001_R1_001.good.fq1,221,803275,881,531100.0%225.8 bases240 bases99.2%
total2,443,606551,939,671100.0%225.9 bases240 bases98.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0212141,869,612292.25.8100.0%Thermotoga maritima MSB8, complete genome.
total1,869,612100.0%

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≤ 1000009611
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 ≤ 500048
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.013

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0212140.68406

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
bowtie22.2.8
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input13:48:56 03 Mar 201813:49:47 03 Mar 201851 seconds
Read alignment to reference genome13:49:47 03 Mar 201813:54:02 03 Mar 20184 minutes 15 seconds
Preprocessing alignments for candidate junction identification13:54:02 03 Mar 201813:55:05 03 Mar 20181 minute 3 seconds
Preliminary analysis of coverage distribution13:55:05 03 Mar 201813:57:24 03 Mar 20182 minutes 19 seconds
Identifying junction candidates13:57:24 03 Mar 201813:57:43 03 Mar 201819 seconds
Re-alignment to junction candidates13:57:43 03 Mar 201813:58:44 03 Mar 20181 minute 1 second
Resolving best read alignments13:58:44 03 Mar 201814:00:34 03 Mar 20181 minute 50 seconds
Creating BAM files14:00:34 03 Mar 201814:02:28 03 Mar 20181 minute 54 seconds
Tabulating error counts14:02:28 03 Mar 201814:03:51 03 Mar 20181 minute 23 seconds
Re-calibrating base error rates14:03:51 03 Mar 201814:03:53 03 Mar 20182 seconds
Examining read alignment evidence14:03:53 03 Mar 201814:19:18 03 Mar 201815 minutes 25 seconds
Polymorphism statistics14:19:18 03 Mar 201814:19:19 03 Mar 20181 second
Output14:19:19 03 Mar 201814:19:43 03 Mar 201824 seconds
Total 30 minutes 47 seconds