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_A1_F070_I0_R1_S18_L004_R1_0012,077,354207,668,184100.0%100.0 bases100 bases97.3%
errorsqtrim-IND_KHP_HOT_A1_F070_I0_R1_S18_L004_R2_0012,077,338207,287,449100.0%99.8 bases100 bases96.4%
total4,154,692414,955,633100.0%99.9 bases100 bases96.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65286.31.998.1%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≤ 10000077334
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 ≤ 50001100
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.049

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.68131

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 input18:52:35 13 Jan 201718:53:18 13 Jan 201743 seconds
Read alignment to reference genome18:53:19 13 Jan 201718:55:39 13 Jan 20172 minutes 20 seconds
Preprocessing alignments for candidate junction identification18:55:39 13 Jan 201718:57:04 13 Jan 20171 minute 25 seconds
Preliminary analysis of coverage distribution18:57:04 13 Jan 201718:58:44 13 Jan 20171 minute 40 seconds
Identifying junction candidates18:58:44 13 Jan 201719:04:57 13 Jan 20176 minutes 13 seconds
Re-alignment to junction candidates19:04:57 13 Jan 201719:05:27 13 Jan 201730 seconds
Resolving alignments with junction candidates19:05:27 13 Jan 201719:07:54 13 Jan 20172 minutes 27 seconds
Creating BAM files19:07:54 13 Jan 201719:08:52 13 Jan 201758 seconds
Tabulating error counts19:08:52 13 Jan 201719:10:40 13 Jan 20171 minute 48 seconds
Re-calibrating base error rates19:10:40 13 Jan 201719:10:40 13 Jan 20170 seconds
Examining read alignment evidence19:10:40 13 Jan 201719:48:01 13 Jan 201737 minutes 21 seconds
Polymorphism statistics19:48:01 13 Jan 201719:48:03 13 Jan 20172 seconds
Output19:48:03 13 Jan 201719:49:05 13 Jan 20171 minute 2 seconds
Total 56 minutes 29 seconds