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_A16_F125_I1_R1_S71_L004_R1_0012,407,275240,660,419100.0%100.0 bases100 bases94.0%
errorsqtrim-IND_KHP_HOT_A16_F125_I1_R1_S71_L004_R2_0012,407,272240,442,884100.0%99.9 bases100 bases93.8%
total4,814,547481,103,303100.0%99.9 bases100 bases93.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65296.71.998.0%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≤ 100000100001
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 ≤ 50001374
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.062

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.65540

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 input23:19:09 04 Jan 201723:19:59 04 Jan 201750 seconds
Read alignment to reference genome23:20:00 04 Jan 201723:22:46 04 Jan 20172 minutes 46 seconds
Preprocessing alignments for candidate junction identification23:22:46 04 Jan 201723:24:27 04 Jan 20171 minute 41 seconds
Preliminary analysis of coverage distribution23:24:27 04 Jan 201723:26:15 04 Jan 20171 minute 48 seconds
Identifying junction candidates23:26:15 04 Jan 201723:35:54 04 Jan 20179 minutes 39 seconds
Re-alignment to junction candidates23:35:54 04 Jan 201723:36:32 04 Jan 201738 seconds
Resolving alignments with junction candidates23:36:32 04 Jan 201723:39:21 04 Jan 20172 minutes 49 seconds
Creating BAM files23:39:21 04 Jan 201723:40:23 04 Jan 20171 minute 2 seconds
Tabulating error counts23:40:23 04 Jan 201723:42:54 04 Jan 20172 minutes 31 seconds
Re-calibrating base error rates23:42:54 04 Jan 201723:42:55 04 Jan 20171 second
Examining read alignment evidence23:42:55 04 Jan 201723:58:55 04 Jan 201716 minutes 0 seconds
Polymorphism statistics23:58:55 04 Jan 201723:58:55 04 Jan 20170 seconds
Output23:58:55 04 Jan 201723:59:48 04 Jan 201753 seconds
Total 40 minutes 38 seconds