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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsD-lyx-PAL-A4-F90-I0-R1_S10_L001_R1_001.good.fq1,391,565416,855,525100.0%299.6 bases300 bases86.2%
errorsD-lyx-PAL-A4-F90-I0-R1_S10_L001_R2_001.good.fq1,193,226340,674,998100.0%285.5 bases286 bases88.5%
total2,584,791757,530,523100.0%293.1 bases300 bases87.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652121.22.3100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 10000011714
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 ≤ 5000498
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.065

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81628

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 input11:29:58 27 Mar 201911:30:52 27 Mar 201954 seconds
Read alignment to reference genome11:30:52 27 Mar 201911:46:33 27 Mar 201915 minutes 41 seconds
Preprocessing alignments for candidate junction identification11:46:33 27 Mar 201911:47:15 27 Mar 201942 seconds
Preliminary analysis of coverage distribution11:47:15 27 Mar 201911:49:37 27 Mar 20192 minutes 22 seconds
Identifying junction candidates11:49:37 27 Mar 201911:49:46 27 Mar 20199 seconds
Re-alignment to junction candidates11:49:46 27 Mar 201911:54:09 27 Mar 20194 minutes 23 seconds
Resolving best read alignments11:54:09 27 Mar 201911:55:27 27 Mar 20191 minute 18 seconds
Creating BAM files11:55:27 27 Mar 201911:57:28 27 Mar 20192 minutes 1 second
Tabulating error counts11:57:28 27 Mar 201911:58:26 27 Mar 201958 seconds
Re-calibrating base error rates11:58:26 27 Mar 201911:58:27 27 Mar 20191 second
Examining read alignment evidence11:58:27 27 Mar 201912:56:58 27 Mar 201958 minutes 31 seconds
Polymorphism statistics12:56:58 27 Mar 201912:56:59 27 Mar 20191 second
Output12:56:59 27 Mar 201912:57:23 27 Mar 201924 seconds
Total 1 hour 27 minutes 25 seconds