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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_TALE__HGL_Pputida_115_S103_L001_R1_001.good.fq6,550,065953,648,667100.0%145.6 bases150 bases95.8%
errorsPputida_TALE__HGL_Pputida_115_S103_L001_R2_001.good.fq6,550,065953,648,667100.0%145.6 bases150 bases95.2%
total13,100,1301,907,297,334100.0%145.6 bases150 bases95.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,929294.55.5100.0%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≤ 100000100000
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 ≤ 50001132
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.057

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.51604

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 input12:13:36 06 Apr 202012:17:05 06 Apr 20203 minutes 29 seconds
Read alignment to reference genome12:17:05 06 Apr 202012:48:49 06 Apr 202031 minutes 44 seconds
Preprocessing alignments for candidate junction identification12:48:49 06 Apr 202012:52:16 06 Apr 20203 minutes 27 seconds
Preliminary analysis of coverage distribution12:52:16 06 Apr 202012:58:34 06 Apr 20206 minutes 18 seconds
Identifying junction candidates12:58:34 06 Apr 202013:07:43 06 Apr 20209 minutes 9 seconds
Re-alignment to junction candidates13:07:43 06 Apr 202013:16:32 06 Apr 20208 minutes 49 seconds
Resolving best read alignments13:16:32 06 Apr 202013:22:47 06 Apr 20206 minutes 15 seconds
Creating BAM files13:22:47 06 Apr 202013:28:09 06 Apr 20205 minutes 22 seconds
Tabulating error counts13:28:09 06 Apr 202013:31:03 06 Apr 20202 minutes 54 seconds
Re-calibrating base error rates13:31:03 06 Apr 202013:31:05 06 Apr 20202 seconds
Examining read alignment evidence13:31:05 06 Apr 202013:59:11 06 Apr 202028 minutes 6 seconds
Polymorphism statistics13:59:11 06 Apr 202013:59:26 06 Apr 202015 seconds
Output13:59:26 06 Apr 202014:00:38 06 Apr 20201 minute 12 seconds
Total 1 hour 47 minutes 2 seconds