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_A12_F133_I0_R1_S57_L004_R1_0014,175,694417,409,963100.0%100.0 bases100 bases95.0%
errorsqtrim-IND_KHP_HOT_A12_F133_I0_R1_S57_L004_R2_0014,175,660415,919,110100.0%99.6 bases100 bases93.7%
total8,351,354833,329,073100.0%99.8 bases100 bases94.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652171.46.598.2%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≤ 100000100090
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 ≤ 50001967
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.088

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.49998

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 input20:33:16 12 Jan 201720:34:45 12 Jan 20171 minute 29 seconds
Read alignment to reference genome20:34:46 12 Jan 201720:39:39 12 Jan 20174 minutes 53 seconds
Preprocessing alignments for candidate junction identification20:39:39 12 Jan 201720:42:35 12 Jan 20172 minutes 56 seconds
Preliminary analysis of coverage distribution20:42:35 12 Jan 201720:45:58 12 Jan 20173 minutes 23 seconds
Identifying junction candidates20:45:58 12 Jan 201721:17:47 12 Jan 201731 minutes 49 seconds
Re-alignment to junction candidates21:17:47 12 Jan 201721:18:58 12 Jan 20171 minute 11 seconds
Resolving alignments with junction candidates21:18:58 12 Jan 201721:23:49 12 Jan 20174 minutes 51 seconds
Creating BAM files21:23:49 12 Jan 201721:25:50 12 Jan 20172 minutes 1 second
Tabulating error counts21:25:50 12 Jan 201721:29:21 12 Jan 20173 minutes 31 seconds
Re-calibrating base error rates21:29:21 12 Jan 201721:29:22 12 Jan 20171 second
Examining read alignment evidence21:29:22 12 Jan 201723:40:07 12 Jan 20172 hours 10 minutes 45 seconds
Polymorphism statistics23:40:07 12 Jan 201723:40:15 12 Jan 20178 seconds
Output23:40:15 12 Jan 201723:42:50 12 Jan 20172 minutes 35 seconds
Total 3 hours 9 minutes 33 seconds