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-ADIP3-4_S7_L001_R1_0011,030,602155,108,677100.0%150.5 bases151 bases99.8%
errorsqtrim-ADIP3-4_S7_L001_R2_0011,030,576155,027,456100.0%150.4 bases151 bases99.2%
total2,061,178310,136,133100.0%150.5 bases151 bases99.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65266.41.298.2%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≤ 1000002704
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 ≤ 500029
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.80956

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 input16:18:53 03 Jan 201716:19:42 03 Jan 201749 seconds
Read alignment to reference genome16:19:43 03 Jan 201716:26:32 03 Jan 20176 minutes 49 seconds
Preprocessing alignments for candidate junction identification16:26:32 03 Jan 201716:27:48 03 Jan 20171 minute 16 seconds
Preliminary analysis of coverage distribution16:27:48 03 Jan 201716:29:48 03 Jan 20172 minutes 0 seconds
Identifying junction candidates16:29:48 03 Jan 201716:29:49 03 Jan 20171 second
Re-alignment to junction candidates16:29:49 03 Jan 201716:31:17 03 Jan 20171 minute 28 seconds
Resolving alignments with junction candidates16:31:17 03 Jan 201716:33:22 03 Jan 20172 minutes 5 seconds
Creating BAM files16:33:22 03 Jan 201716:34:53 03 Jan 20171 minute 31 seconds
Tabulating error counts16:34:53 03 Jan 201716:36:40 03 Jan 20171 minute 47 seconds
Re-calibrating base error rates16:36:40 03 Jan 201716:36:42 03 Jan 20172 seconds
Examining read alignment evidence16:36:42 03 Jan 201716:51:44 03 Jan 201715 minutes 2 seconds
Polymorphism statistics16:51:44 03 Jan 201716:51:45 03 Jan 20171 second
Output16:51:45 03 Jan 201716:52:11 03 Jan 201726 seconds
Total 33 minutes 17 seconds