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_A10_F044_I0_R1_S50_L004_R2_0013,881,346386,783,868100.0%99.7 bases100 bases94.0%
errorsqtrim-IND_KHP_HOT_A10_F044_I0_R1_S50_L004_R1_0013,881,378387,992,951100.0%100.0 bases100 bases95.0%
total7,762,724774,776,819100.0%99.8 bases100 bases94.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652156.12.298.2%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≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000702
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.032

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.52031

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 input06:58:28 13 Jan 201706:59:52 13 Jan 20171 minute 24 seconds
Read alignment to reference genome06:59:52 13 Jan 201707:04:22 13 Jan 20174 minutes 30 seconds
Preprocessing alignments for candidate junction identification07:04:22 13 Jan 201707:07:09 13 Jan 20172 minutes 47 seconds
Preliminary analysis of coverage distribution07:07:09 13 Jan 201707:10:15 13 Jan 20173 minutes 6 seconds
Identifying junction candidates07:10:15 13 Jan 201707:13:26 13 Jan 20173 minutes 11 seconds
Re-alignment to junction candidates07:13:26 13 Jan 201707:14:18 13 Jan 201752 seconds
Resolving alignments with junction candidates07:14:18 13 Jan 201707:18:52 13 Jan 20174 minutes 34 seconds
Creating BAM files07:18:52 13 Jan 201707:20:43 13 Jan 20171 minute 51 seconds
Tabulating error counts07:20:43 13 Jan 201707:23:58 13 Jan 20173 minutes 15 seconds
Re-calibrating base error rates07:23:58 13 Jan 201707:23:59 13 Jan 20171 second
Examining read alignment evidence07:23:59 13 Jan 201709:14:35 13 Jan 20171 hour 50 minutes 36 seconds
Polymorphism statistics09:14:35 13 Jan 201709:14:41 13 Jan 20176 seconds
Output09:14:41 13 Jan 201709:15:49 13 Jan 20171 minute 8 seconds
Total 2 hours 17 minutes 21 seconds