breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-IND_KHP_HOT_A16_F201_I0_R1_S86_L004_R2_0014,415,655439,958,852100.0%99.6 bases100 bases92.5%
errorsqtrim-IND_KHP_HOT_A16_F201_I0_R1_S86_L004_R1_0014,415,687441,405,655100.0%100.0 bases100 bases94.2%
total8,831,342881,364,507100.0%99.8 bases100 bases93.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652176.93.098.1%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≤ 100000100021
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 ≤ 50002100
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.094

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.48586

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 cutoffOFF
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.15
Polymorphism minimum coverage each strand2
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 ≥2 bases

Execution Times

stepstartendelapsed
Read and reference sequence file input21:44:29 10 Jan 201721:46:07 10 Jan 20171 minute 38 seconds
Read alignment to reference genome21:46:07 10 Jan 201721:52:14 10 Jan 20176 minutes 7 seconds
Preprocessing alignments for candidate junction identification21:52:14 10 Jan 201721:55:32 10 Jan 20173 minutes 18 seconds
Preliminary analysis of coverage distribution21:55:32 10 Jan 201721:59:14 10 Jan 20173 minutes 42 seconds
Identifying junction candidates21:59:14 10 Jan 201722:27:44 10 Jan 201728 minutes 30 seconds
Re-alignment to junction candidates22:27:44 10 Jan 201722:29:10 10 Jan 20171 minute 26 seconds
Resolving alignments with junction candidates22:29:10 10 Jan 201722:34:32 10 Jan 20175 minutes 22 seconds
Creating BAM files22:34:32 10 Jan 201722:36:43 10 Jan 20172 minutes 11 seconds
Tabulating error counts22:36:43 10 Jan 201722:41:04 10 Jan 20174 minutes 21 seconds
Re-calibrating base error rates22:41:04 10 Jan 201722:41:06 10 Jan 20172 seconds
Examining read alignment evidence22:41:06 10 Jan 201701:11:19 11 Jan 20172 hours 30 minutes 13 seconds
Polymorphism statistics01:11:19 11 Jan 201701:11:27 11 Jan 20178 seconds
Output01:11:27 11 Jan 201701:15:07 11 Jan 20173 minutes 40 seconds
Total 3 hours 30 minutes 38 seconds