breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1957986_R1.good.fq361,22681,082,713100.0%224.5 bases240 bases99.1%
errorsERR1957986_R2.good.fq361,21571,069,464100.0%196.8 bases240 bases95.3%
total722,441152,152,177100.0%210.6 bases240 bases97.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65229.82.493.6%Escherichia coli str. K-12 substr. MG1655, complete genome.
coveragedistributionBN00092560,096166.06.36.4%TPA_exp: Birmingham IncP-alpha plasmid, complete sequence, isolate
total4,701,748100.0%

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≤ 1000001838
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 ≤ 500064
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.94075
BN0009250.77475

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 cutoff0.75
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input14:44:10 08 Dec 202014:45:02 08 Dec 202052 seconds
Read alignment to reference genome14:45:03 08 Dec 202014:53:43 08 Dec 20208 minutes 40 seconds
Preprocessing alignments for candidate junction identification14:53:43 08 Dec 202014:54:18 08 Dec 202035 seconds
Preliminary analysis of coverage distribution14:54:18 08 Dec 202014:56:21 08 Dec 20202 minutes 3 seconds
Identifying junction candidates14:56:21 08 Dec 202014:56:23 08 Dec 20202 seconds
Re-alignment to junction candidates14:56:23 08 Dec 202014:58:44 08 Dec 20202 minutes 21 seconds
Resolving best read alignments14:58:44 08 Dec 202014:59:36 08 Dec 202052 seconds
Creating BAM files14:59:36 08 Dec 202015:01:20 08 Dec 20201 minute 44 seconds
Tabulating error counts15:01:20 08 Dec 202015:02:02 08 Dec 202042 seconds
Re-calibrating base error rates15:02:02 08 Dec 202015:02:07 08 Dec 20205 seconds
Examining read alignment evidence15:02:07 08 Dec 202015:11:50 08 Dec 20209 minutes 43 seconds
Polymorphism statistics15:11:50 08 Dec 202015:11:51 08 Dec 20201 second
Output15:11:51 08 Dec 202015:12:35 08 Dec 202044 seconds
Total 28 minutes 24 seconds