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_A4_F191_I1_R1_S17_L004_R1_0012,767,631276,682,656100.0%100.0 bases100 bases93.2%
errorsqtrim-IND_KHP_HOT_A4_F191_I1_R1_S17_L004_R2_0012,767,612276,375,141100.0%99.9 bases100 bases92.3%
total5,535,243553,057,797100.0%99.9 bases100 bases92.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652105.92.798.2%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≤ 10000034657
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50001256
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.056

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.62198

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≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Execution Times

stepstartendelapsed
Read and reference sequence file input10:22:10 05 Jan 201710:23:07 05 Jan 201757 seconds
Read alignment to reference genome10:23:07 05 Jan 201710:26:17 05 Jan 20173 minutes 10 seconds
Preprocessing alignments for candidate junction identification10:26:17 05 Jan 201710:28:08 05 Jan 20171 minute 51 seconds
Preliminary analysis of coverage distribution10:28:08 05 Jan 201710:30:11 05 Jan 20172 minutes 3 seconds
Identifying junction candidates10:30:11 05 Jan 201710:31:28 05 Jan 20171 minute 17 seconds
Re-alignment to junction candidates10:31:28 05 Jan 201710:32:08 05 Jan 201740 seconds
Resolving alignments with junction candidates10:32:08 05 Jan 201710:35:18 05 Jan 20173 minutes 10 seconds
Creating BAM files10:35:18 05 Jan 201710:36:29 05 Jan 20171 minute 11 seconds
Tabulating error counts10:36:29 05 Jan 201710:38:47 05 Jan 20172 minutes 18 seconds
Re-calibrating base error rates10:38:47 05 Jan 201710:38:47 05 Jan 20170 seconds
Examining read alignment evidence10:38:47 05 Jan 201710:55:43 05 Jan 201716 minutes 56 seconds
Polymorphism statistics10:55:43 05 Jan 201710:55:43 05 Jan 20170 seconds
Output10:55:43 05 Jan 201710:56:23 05 Jan 201740 seconds
Total 34 minutes 13 seconds