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_A9_F200_I0_R1_S41_L004_R1_0012,604,966260,402,924100.0%100.0 bases100 bases95.3%
errorsqtrim-IND_KHP_HOT_A9_F200_I0_R1_S41_L004_R2_0012,604,953259,643,795100.0%99.7 bases100 bases93.5%
total5,209,919520,046,719100.0%99.8 bases100 bases94.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652105.45.498.0%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≤ 100000100142
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 ≤ 5000610
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.027

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.63551

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 input15:46:48 12 Jan 201715:47:42 12 Jan 201754 seconds
Read alignment to reference genome15:47:42 12 Jan 201715:50:45 12 Jan 20173 minutes 3 seconds
Preprocessing alignments for candidate junction identification15:50:45 12 Jan 201715:52:39 12 Jan 20171 minute 54 seconds
Preliminary analysis of coverage distribution15:52:39 12 Jan 201715:54:44 12 Jan 20172 minutes 5 seconds
Identifying junction candidates15:54:44 12 Jan 201715:56:40 12 Jan 20171 minute 56 seconds
Re-alignment to junction candidates15:56:40 12 Jan 201715:57:47 12 Jan 20171 minute 7 seconds
Resolving alignments with junction candidates15:57:47 12 Jan 201716:02:18 12 Jan 20174 minutes 31 seconds
Creating BAM files16:02:18 12 Jan 201716:03:34 12 Jan 20171 minute 16 seconds
Tabulating error counts16:03:34 12 Jan 201716:06:02 12 Jan 20172 minutes 28 seconds
Re-calibrating base error rates16:06:02 12 Jan 201716:06:03 12 Jan 20171 second
Examining read alignment evidence16:06:03 12 Jan 201717:04:30 12 Jan 201758 minutes 27 seconds
Polymorphism statistics17:04:30 12 Jan 201717:04:34 12 Jan 20174 seconds
Output17:04:34 12 Jan 201717:05:46 12 Jan 20171 minute 12 seconds
Total 1 hour 18 minutes 58 seconds