breseq  version 0.33.2  revision caddc01d3be9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_HGL_47_S259_L002_R1_001.good.fq2,511,223340,118,734100.0%135.4 bases150 bases96.0%
errorsPputida_HGL_47_S259_L002_R2_001.good.fq2,511,223340,118,734100.0%135.4 bases150 bases94.3%
total5,022,446680,237,468100.0%135.4 bases150 bases95.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,929104.73.5100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,181,929100.0%

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≤ 10000052136
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 ≤ 5000776
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.039

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.71197

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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input00:14:42 21 Aug 201900:16:44 21 Aug 20192 minutes 2 seconds
Read alignment to reference genome00:16:45 21 Aug 201900:34:34 21 Aug 201917 minutes 49 seconds
Preprocessing alignments for candidate junction identification00:34:34 21 Aug 201900:36:23 21 Aug 20191 minute 49 seconds
Preliminary analysis of coverage distribution00:36:23 21 Aug 201900:40:05 21 Aug 20193 minutes 42 seconds
Identifying junction candidates00:40:05 21 Aug 201901:11:29 21 Aug 201931 minutes 24 seconds
Re-alignment to junction candidates01:11:29 21 Aug 201901:16:38 21 Aug 20195 minutes 9 seconds
Resolving best read alignments01:16:38 21 Aug 201901:19:21 21 Aug 20192 minutes 43 seconds
Creating BAM files01:19:21 21 Aug 201901:22:36 21 Aug 20193 minutes 15 seconds
Tabulating error counts01:22:36 21 Aug 201901:24:17 21 Aug 20191 minute 41 seconds
Re-calibrating base error rates01:24:17 21 Aug 201901:24:18 21 Aug 20191 second
Examining read alignment evidence01:24:18 21 Aug 201901:46:19 21 Aug 201922 minutes 1 second
Polymorphism statistics01:46:19 21 Aug 201901:46:20 21 Aug 20191 second
Output01:46:20 21 Aug 201901:47:15 21 Aug 201955 seconds
Total 1 hour 32 minutes 32 seconds