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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR5762419_R1.good.fq58,112,2943,921,554,728100.0%67.5 bases68 bases99.2%
total58,112,2943,921,554,728100.0%67.5 bases68 bases99.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0092734,631,469835.851.8100.0%Escherichia coli BW25113, complete genome.
total4,631,469100.0%

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≤ 10000072485
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 ≤ 50001404
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.044

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0092730.42837

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≤ 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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input11:39:38 03 May 202111:52:45 03 May 202113 minutes 7 seconds
Read alignment to reference genome11:52:45 03 May 202112:57:48 03 May 20211 hour 5 minutes 3 seconds
Preprocessing alignments for candidate junction identification12:57:48 03 May 202113:10:23 03 May 202112 minutes 35 seconds
Preliminary analysis of coverage distribution13:10:23 03 May 202113:28:16 03 May 202117 minutes 53 seconds
Identifying junction candidates13:28:16 03 May 202113:33:04 03 May 20214 minutes 48 seconds
Re-alignment to junction candidates13:33:04 03 May 202113:49:59 03 May 202116 minutes 55 seconds
Resolving best read alignments13:49:59 03 May 202114:05:30 03 May 202115 minutes 31 seconds
Creating BAM files14:05:30 03 May 202114:21:32 03 May 202116 minutes 2 seconds
Tabulating error counts14:21:32 03 May 202114:27:25 03 May 20215 minutes 53 seconds
Re-calibrating base error rates14:27:25 03 May 202114:27:26 03 May 20211 second
Examining read alignment evidence14:27:26 03 May 202123:39:28 03 May 20219 hours 12 minutes 2 seconds
Polymorphism statistics23:39:28 03 May 202123:39:29 03 May 20211 second
Output23:39:29 03 May 202123:42:27 03 May 20212 minutes 58 seconds
Total 12 hours 2 minutes 49 seconds