breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-9_S9_L001_R1_001.good.fq309,42944,076,740100.0%142.4 bases149 bases93.2%
errorsALE-9_S9_L001_R2_001.good.fq309,42943,893,786100.0%141.9 bases149 bases93.8%
errorsALE-9_S9_L002_R1_001.good.fq303,33943,149,435100.0%142.2 bases149 bases94.5%
errorsALE-9_S9_L002_R2_001.good.fq303,33943,014,730100.0%141.8 bases149 bases94.2%
errorsALE-9_S9_L003_R1_001.good.fq313,73744,573,014100.0%142.1 bases149 bases94.3%
errorsALE-9_S9_L003_R2_001.good.fq313,73744,405,055100.0%141.5 bases149 bases94.8%
errorsALE-9_S9_L004_R1_001.good.fq293,62541,714,428100.0%142.1 bases149 bases94.3%
errorsALE-9_S9_L004_R2_001.good.fq293,62541,576,447100.0%141.6 bases149 bases93.9%
total2,440,260346,403,635100.0%142.0 bases149 bases94.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,87353.92.8100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,181,873100.0%

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≤ 10000063574
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 ≤ 5000672
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.033

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.84274

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input15:57:14 18 Feb 202015:57:51 18 Feb 202037 seconds
Read alignment to reference genome15:57:51 18 Feb 202016:03:22 18 Feb 20205 minutes 31 seconds
Preprocessing alignments for candidate junction identification16:03:22 18 Feb 202016:03:56 18 Feb 202034 seconds
Preliminary analysis of coverage distribution16:03:56 18 Feb 202016:05:19 18 Feb 20201 minute 23 seconds
Identifying junction candidates16:05:19 18 Feb 202016:12:31 18 Feb 20207 minutes 12 seconds
Re-alignment to junction candidates16:12:31 18 Feb 202016:14:19 18 Feb 20201 minute 48 seconds
Resolving best read alignments16:14:19 18 Feb 202016:15:13 18 Feb 202054 seconds
Creating BAM files16:15:13 18 Feb 202016:16:31 18 Feb 20201 minute 18 seconds
Tabulating error counts16:16:31 18 Feb 202016:16:56 18 Feb 202025 seconds
Re-calibrating base error rates16:16:56 18 Feb 202016:16:59 18 Feb 20203 seconds
Examining read alignment evidence16:16:59 18 Feb 202016:29:29 18 Feb 202012 minutes 30 seconds
Polymorphism statistics16:29:29 18 Feb 202016:29:31 18 Feb 20202 seconds
Output16:29:31 18 Feb 202016:33:58 18 Feb 20204 minutes 27 seconds
Total 36 minutes 44 seconds