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_A6_F078_I0_R1_S34_L004_R2_0013,735,859372,576,623100.0%99.7 bases100 bases91.8%
errorsqtrim-IND_KHP_HOT_A6_F078_I0_R1_S34_L004_R1_0013,735,887373,461,479100.0%100.0 bases100 bases93.0%
total7,471,746746,038,102100.0%99.8 bases100 bases92.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652149.34.498.1%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≤ 100000100000
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 ≤ 50001993
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.089

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.54156

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 input06:24:02 11 Jan 201706:25:25 11 Jan 20171 minute 23 seconds
Read alignment to reference genome06:25:25 11 Jan 201706:30:32 11 Jan 20175 minutes 7 seconds
Preprocessing alignments for candidate junction identification06:30:32 11 Jan 201706:33:22 11 Jan 20172 minutes 50 seconds
Preliminary analysis of coverage distribution06:33:22 11 Jan 201706:36:21 11 Jan 20172 minutes 59 seconds
Identifying junction candidates06:36:21 11 Jan 201707:01:23 11 Jan 201725 minutes 2 seconds
Re-alignment to junction candidates07:01:23 11 Jan 201707:03:31 11 Jan 20172 minutes 8 seconds
Resolving alignments with junction candidates07:03:31 11 Jan 201707:10:08 11 Jan 20176 minutes 37 seconds
Creating BAM files07:10:08 11 Jan 201707:11:56 11 Jan 20171 minute 48 seconds
Tabulating error counts07:11:56 11 Jan 201707:15:35 11 Jan 20173 minutes 39 seconds
Re-calibrating base error rates07:15:35 11 Jan 201707:15:37 11 Jan 20172 seconds
Examining read alignment evidence07:15:37 11 Jan 201708:55:38 11 Jan 20171 hour 40 minutes 1 second
Polymorphism statistics08:55:38 11 Jan 201708:55:43 11 Jan 20175 seconds
Output08:55:43 11 Jan 201708:58:02 11 Jan 20172 minutes 19 seconds
Total 2 hours 34 minutes 0 seconds