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_A3_F228_I0_R1_S73_L004_R2_0012,909,456290,072,443100.0%99.7 bases100 bases93.0%
errorsqtrim-IND_KHP_HOT_A3_F228_I0_R1_S73_L004_R1_0012,909,468290,840,533100.0%100.0 bases100 bases94.2%
total5,818,924580,912,976100.0%99.8 bases100 bases93.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652117.22.398.0%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≤ 100000100009
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 ≤ 50002224
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.099

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.60580

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 input17:18:29 14 Jan 201717:19:29 14 Jan 20171 minute 0 seconds
Read alignment to reference genome17:19:30 14 Jan 201717:22:22 14 Jan 20172 minutes 52 seconds
Preprocessing alignments for candidate junction identification17:22:22 14 Jan 201717:24:28 14 Jan 20172 minutes 6 seconds
Preliminary analysis of coverage distribution17:24:28 14 Jan 201717:26:46 14 Jan 20172 minutes 18 seconds
Identifying junction candidates17:26:46 14 Jan 201717:48:48 14 Jan 201722 minutes 2 seconds
Re-alignment to junction candidates17:48:48 14 Jan 201717:49:32 14 Jan 201744 seconds
Resolving alignments with junction candidates17:49:32 14 Jan 201717:53:02 14 Jan 20173 minutes 30 seconds
Creating BAM files17:53:02 14 Jan 201717:54:24 14 Jan 20171 minute 22 seconds
Tabulating error counts17:54:24 14 Jan 201717:56:52 14 Jan 20172 minutes 28 seconds
Re-calibrating base error rates17:56:52 14 Jan 201717:56:52 14 Jan 20170 seconds
Examining read alignment evidence17:56:52 14 Jan 201719:02:38 14 Jan 20171 hour 5 minutes 46 seconds
Polymorphism statistics19:02:38 14 Jan 201719:02:43 14 Jan 20175 seconds
Output19:02:43 14 Jan 201719:05:32 14 Jan 20172 minutes 49 seconds
Total 1 hour 47 minutes 2 seconds