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_A14_F129_I0_R1_S82_L004_R1_0013,950,754394,933,222100.0%100.0 bases100 bases94.5%
errorsqtrim-IND_KHP_HOT_A14_F129_I0_R1_S82_L004_R2_0013,950,724393,781,313100.0%99.7 bases100 bases93.1%
total7,901,478788,714,535100.0%99.8 bases100 bases93.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652159.32.298.1%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≤ 100000100081
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000674
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.030

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.51643

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 input08:16:22 14 Jan 201708:17:49 14 Jan 20171 minute 27 seconds
Read alignment to reference genome08:17:50 14 Jan 201708:21:46 14 Jan 20173 minutes 56 seconds
Preprocessing alignments for candidate junction identification08:21:46 14 Jan 201708:24:40 14 Jan 20172 minutes 54 seconds
Preliminary analysis of coverage distribution08:24:40 14 Jan 201708:27:46 14 Jan 20173 minutes 6 seconds
Identifying junction candidates08:27:46 14 Jan 201708:29:41 14 Jan 20171 minute 55 seconds
Re-alignment to junction candidates08:29:41 14 Jan 201708:30:28 14 Jan 201747 seconds
Resolving alignments with junction candidates08:30:28 14 Jan 201708:35:10 14 Jan 20174 minutes 42 seconds
Creating BAM files08:35:10 14 Jan 201708:36:59 14 Jan 20171 minute 49 seconds
Tabulating error counts08:36:59 14 Jan 201708:40:17 14 Jan 20173 minutes 18 seconds
Re-calibrating base error rates08:40:17 14 Jan 201708:40:17 14 Jan 20170 seconds
Examining read alignment evidence08:40:17 14 Jan 201710:25:38 14 Jan 20171 hour 45 minutes 21 seconds
Polymorphism statistics10:25:38 14 Jan 201710:25:45 14 Jan 20177 seconds
Output10:25:45 14 Jan 201710:27:24 14 Jan 20171 minute 39 seconds
Total 2 hours 11 minutes 1 second