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_A11_F256_I0_R1_S78_L004_R1_0012,561,577256,064,780100.0%100.0 bases100 bases94.3%
errorsqtrim-IND_KHP_HOT_A11_F256_I0_R1_S78_L004_R2_0012,561,561255,229,906100.0%99.6 bases100 bases92.6%
total5,123,138511,294,686100.0%99.8 bases100 bases93.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652102.71.798.1%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≤ 100000100013
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 ≤ 5000534
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.024

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.63940

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 input01:15:08 11 Jan 201701:16:03 11 Jan 201755 seconds
Read alignment to reference genome01:16:03 11 Jan 201701:19:31 11 Jan 20173 minutes 28 seconds
Preprocessing alignments for candidate junction identification01:19:31 11 Jan 201701:21:24 11 Jan 20171 minute 53 seconds
Preliminary analysis of coverage distribution01:21:24 11 Jan 201701:23:32 11 Jan 20172 minutes 8 seconds
Identifying junction candidates01:23:32 11 Jan 201701:25:46 11 Jan 20172 minutes 14 seconds
Re-alignment to junction candidates01:25:46 11 Jan 201701:26:25 11 Jan 201739 seconds
Resolving alignments with junction candidates01:26:25 11 Jan 201701:29:30 11 Jan 20173 minutes 5 seconds
Creating BAM files01:29:30 11 Jan 201701:30:47 11 Jan 20171 minute 17 seconds
Tabulating error counts01:30:47 11 Jan 201701:33:02 11 Jan 20172 minutes 15 seconds
Re-calibrating base error rates01:33:02 11 Jan 201701:33:03 11 Jan 20171 second
Examining read alignment evidence01:33:03 11 Jan 201702:39:24 11 Jan 20171 hour 6 minutes 21 seconds
Polymorphism statistics02:39:24 11 Jan 201702:39:28 11 Jan 20174 seconds
Output02:39:28 11 Jan 201702:41:17 11 Jan 20171 minute 49 seconds
Total 1 hour 26 minutes 9 seconds