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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors4-195_S4_L001_R1_001_150209.good.fq609,280155,841,768100.0%255.8 bases275 bases98.2%
errors4-195_S4_L001_R1_001_150513.good.fq512,945133,165,379100.0%259.6 bases275 bases97.9%
errors4-195_S4_L001_R2_001_150209.good.fq609,280156,338,128100.0%256.6 bases275 bases85.2%
errors4-195_S4_L001_R2_001_150513.good.fq512,945134,009,783100.0%261.3 bases275 bases66.2%
total2,244,450579,355,058100.0%258.1 bases275 bases87.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652105.54.2100.0%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≤ 1000003698
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 ≤ 5000180
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.022

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.87214

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 input00:38:24 08 Jan 201900:39:10 08 Jan 201946 seconds
Read alignment to reference genome00:39:10 08 Jan 201900:53:55 08 Jan 201914 minutes 45 seconds
Preprocessing alignments for candidate junction identification00:53:55 08 Jan 201900:54:30 08 Jan 201935 seconds
Preliminary analysis of coverage distribution00:54:30 08 Jan 201900:56:34 08 Jan 20192 minutes 4 seconds
Identifying junction candidates00:56:34 08 Jan 201900:56:39 08 Jan 20195 seconds
Re-alignment to junction candidates00:56:39 08 Jan 201900:59:14 08 Jan 20192 minutes 35 seconds
Resolving best read alignments00:59:14 08 Jan 201901:00:18 08 Jan 20191 minute 4 seconds
Creating BAM files01:00:18 08 Jan 201901:02:04 08 Jan 20191 minute 46 seconds
Tabulating error counts01:02:04 08 Jan 201901:02:52 08 Jan 201948 seconds
Re-calibrating base error rates01:02:52 08 Jan 201901:02:54 08 Jan 20192 seconds
Examining read alignment evidence01:02:54 08 Jan 201901:11:33 08 Jan 20198 minutes 39 seconds
Polymorphism statistics01:11:33 08 Jan 201901:11:33 08 Jan 20190 seconds
Output01:11:33 08 Jan 201901:11:47 08 Jan 201914 seconds
Total 33 minutes 23 seconds