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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR2168726_R1.good.fq1,475,82998,109,668100.0%66.5 bases68 bases93.6%
errorsSRR2168726_R2.good.fq1,475,82498,109,328100.0%66.5 bases68 bases92.9%
total2,951,653196,218,996100.0%66.5 bases68 bases93.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65239.42.7100.0%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≤ 10000056647
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 ≤ 5000213
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_0009130.82052

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 input14:35:31 03 Mar 202014:36:08 03 Mar 202037 seconds
Read alignment to reference genome14:36:09 03 Mar 202014:41:58 03 Mar 20205 minutes 49 seconds
Preprocessing alignments for candidate junction identification14:41:58 03 Mar 202014:42:41 03 Mar 202043 seconds
Preliminary analysis of coverage distribution14:42:41 03 Mar 202014:43:37 03 Mar 202056 seconds
Identifying junction candidates14:43:37 03 Mar 202014:44:03 03 Mar 202026 seconds
Re-alignment to junction candidates14:44:03 03 Mar 202014:44:55 03 Mar 202052 seconds
Resolving best read alignments14:44:55 03 Mar 202014:45:54 03 Mar 202059 seconds
Creating BAM files14:45:54 03 Mar 202014:46:55 03 Mar 20201 minute 1 second
Tabulating error counts14:46:55 03 Mar 202014:47:11 03 Mar 202016 seconds
Re-calibrating base error rates14:47:11 03 Mar 202014:47:12 03 Mar 20201 second
Examining read alignment evidence14:47:12 03 Mar 202014:50:28 03 Mar 20203 minutes 16 seconds
Polymorphism statistics14:50:28 03 Mar 202014:50:29 03 Mar 20201 second
Output14:50:29 03 Mar 202014:50:50 03 Mar 202021 seconds
Total 15 minutes 18 seconds