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_A8_F120_I0_R1_S37_L004_R2_0013,705,448369,208,529100.0%99.6 bases100 bases92.5%
errorsqtrim-IND_KHP_HOT_A8_F120_I0_R1_S37_L004_R1_0013,705,477370,411,733100.0%100.0 bases100 bases94.1%
total7,410,925739,620,262100.0%99.8 bases100 bases93.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652148.34.898.1%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 ≤ 50002195
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.098

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.54053

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 input12:18:43 12 Jan 201712:20:02 12 Jan 20171 minute 19 seconds
Read alignment to reference genome12:20:03 12 Jan 201712:24:25 12 Jan 20174 minutes 22 seconds
Preprocessing alignments for candidate junction identification12:24:25 12 Jan 201712:27:05 12 Jan 20172 minutes 40 seconds
Preliminary analysis of coverage distribution12:27:05 12 Jan 201712:30:04 12 Jan 20172 minutes 59 seconds
Identifying junction candidates12:30:04 12 Jan 201712:59:15 12 Jan 201729 minutes 11 seconds
Re-alignment to junction candidates12:59:15 12 Jan 201713:00:17 12 Jan 20171 minute 2 seconds
Resolving alignments with junction candidates13:00:17 12 Jan 201713:05:00 12 Jan 20174 minutes 43 seconds
Creating BAM files13:05:00 12 Jan 201713:06:48 12 Jan 20171 minute 48 seconds
Tabulating error counts13:06:48 12 Jan 201713:09:53 12 Jan 20173 minutes 5 seconds
Re-calibrating base error rates13:09:53 12 Jan 201713:09:53 12 Jan 20170 seconds
Examining read alignment evidence13:09:53 12 Jan 201714:51:11 12 Jan 20171 hour 41 minutes 18 seconds
Polymorphism statistics14:51:11 12 Jan 201714:51:16 12 Jan 20175 seconds
Output14:51:16 12 Jan 201714:53:45 12 Jan 20172 minutes 29 seconds
Total 2 hours 35 minutes 1 second