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_F050_I0_R1_S36_L004_R2_0013,421,846341,238,785100.0%99.7 bases100 bases93.9%
errorsqtrim-IND_KHP_HOT_A8_F050_I0_R1_S36_L004_R1_0013,421,870342,068,708100.0%100.0 bases100 bases95.1%
total6,843,716683,307,493100.0%99.8 bases100 bases94.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652138.61.998.2%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≤ 100000100023
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 ≤ 50001987
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.089

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.55848

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 input10:27:27 14 Jan 201710:28:42 14 Jan 20171 minute 15 seconds
Read alignment to reference genome10:28:42 14 Jan 201710:32:04 14 Jan 20173 minutes 22 seconds
Preprocessing alignments for candidate junction identification10:32:04 14 Jan 201710:34:39 14 Jan 20172 minutes 35 seconds
Preliminary analysis of coverage distribution10:34:39 14 Jan 201710:37:19 14 Jan 20172 minutes 40 seconds
Identifying junction candidates10:37:19 14 Jan 201710:58:45 14 Jan 201721 minutes 26 seconds
Re-alignment to junction candidates10:58:45 14 Jan 201710:59:33 14 Jan 201748 seconds
Resolving alignments with junction candidates10:59:33 14 Jan 201711:03:36 14 Jan 20174 minutes 3 seconds
Creating BAM files11:03:36 14 Jan 201711:05:09 14 Jan 20171 minute 33 seconds
Tabulating error counts11:05:09 14 Jan 201711:08:03 14 Jan 20172 minutes 54 seconds
Re-calibrating base error rates11:08:03 14 Jan 201711:08:03 14 Jan 20170 seconds
Examining read alignment evidence11:08:03 14 Jan 201712:27:36 14 Jan 20171 hour 19 minutes 33 seconds
Polymorphism statistics12:27:36 14 Jan 201712:27:41 14 Jan 20175 seconds
Output12:27:41 14 Jan 201712:29:54 14 Jan 20172 minutes 13 seconds
Total 2 hours 2 minutes 27 seconds