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_A15_F055_I0_R1_S83_L004_R1_0013,646,645364,524,885100.0%100.0 bases100 bases94.0%
errorsqtrim-IND_KHP_HOT_A15_F055_I0_R1_S83_L004_R2_0013,646,617363,237,334100.0%99.6 bases100 bases92.0%
total7,293,262727,762,219100.0%99.8 bases100 bases93.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652145.62.098.1%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≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000625
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.028

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.54256

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 input00:30:16 14 Jan 201700:31:35 14 Jan 20171 minute 19 seconds
Read alignment to reference genome00:31:36 14 Jan 201700:35:26 14 Jan 20173 minutes 50 seconds
Preprocessing alignments for candidate junction identification00:35:26 14 Jan 201700:38:08 14 Jan 20172 minutes 42 seconds
Preliminary analysis of coverage distribution00:38:08 14 Jan 201700:41:02 14 Jan 20172 minutes 54 seconds
Identifying junction candidates00:41:02 14 Jan 201700:42:50 14 Jan 20171 minute 48 seconds
Re-alignment to junction candidates00:42:50 14 Jan 201700:43:32 14 Jan 201742 seconds
Resolving alignments with junction candidates00:43:32 14 Jan 201700:47:54 14 Jan 20174 minutes 22 seconds
Creating BAM files00:47:54 14 Jan 201700:49:36 14 Jan 20171 minute 42 seconds
Tabulating error counts00:49:36 14 Jan 201700:52:40 14 Jan 20173 minutes 4 seconds
Re-calibrating base error rates00:52:40 14 Jan 201700:52:41 14 Jan 20171 second
Examining read alignment evidence00:52:41 14 Jan 201702:33:56 14 Jan 20171 hour 41 minutes 15 seconds
Polymorphism statistics02:33:56 14 Jan 201702:34:02 14 Jan 20176 seconds
Output02:34:02 14 Jan 201702:35:49 14 Jan 20171 minute 47 seconds
Total 2 hours 5 minutes 32 seconds