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_F255_I0_R1_S76_L004_R1_0012,250,239224,689,036100.0%99.9 bases100 bases95.9%
errorsqtrim-IND_KHP_HOT_A9_F255_I0_R1_S76_L004_R2_0012,250,224224,239,438100.0%99.7 bases100 bases94.3%
total4,500,463448,928,474100.0%99.8 bases100 bases95.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65291.81.698.1%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≤ 100000100030
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 ≤ 50001878
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.084

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.66670

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 input14:23:57 14 Jan 201714:24:44 14 Jan 201747 seconds
Read alignment to reference genome14:24:45 14 Jan 201714:26:58 14 Jan 20172 minutes 13 seconds
Preprocessing alignments for candidate junction identification14:26:58 14 Jan 201714:28:35 14 Jan 20171 minute 37 seconds
Preliminary analysis of coverage distribution14:28:35 14 Jan 201714:30:26 14 Jan 20171 minute 51 seconds
Identifying junction candidates14:30:26 14 Jan 201714:50:05 14 Jan 201719 minutes 39 seconds
Re-alignment to junction candidates14:50:05 14 Jan 201714:50:36 14 Jan 201731 seconds
Resolving alignments with junction candidates14:50:36 14 Jan 201714:53:18 14 Jan 20172 minutes 42 seconds
Creating BAM files14:53:18 14 Jan 201714:54:25 14 Jan 20171 minute 7 seconds
Tabulating error counts14:54:25 14 Jan 201714:56:19 14 Jan 20171 minute 54 seconds
Re-calibrating base error rates14:56:19 14 Jan 201714:56:20 14 Jan 20171 second
Examining read alignment evidence14:56:20 14 Jan 201715:48:10 14 Jan 201751 minutes 50 seconds
Polymorphism statistics15:48:10 14 Jan 201715:48:13 14 Jan 20173 seconds
Output15:48:13 14 Jan 201715:50:19 14 Jan 20172 minutes 6 seconds
Total 1 hour 26 minutes 21 seconds