breseq  version 0.28.1  revision 52323b585d6f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL20_S28_L001_R1_0011,965,160295,826,78899.7%150.5 bases151 bases99.2%
errorsALE-IL20_S28_L001_R2_0011,963,976295,640,12999.6%150.5 bases151 bases97.7%
errorsALE-IL20_S28_L002_R1_0011,954,854294,287,41599.7%150.5 bases151 bases99.2%
errorsALE-IL20_S28_L002_R2_0011,953,394294,055,50499.7%150.5 bases151 bases97.7%
errorsALE-IL20_S28_L003_R1_0011,988,283299,329,19099.9%150.5 bases151 bases99.1%
errorsALE-IL20_S28_L003_R2_0011,986,293298,995,74599.8%150.5 bases151 bases97.4%
errorsALE-IL20_S28_L004_R1_0011,981,578298,342,39699.9%150.6 bases151 bases99.1%
errorsALE-IL20_S28_L004_R2_0011,978,765297,899,12699.7%150.5 bases151 bases97.9%
total15,772,3032,374,376,29399.7%150.5 bases151 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707504.910.598.2%Escherichia coli DH1, complete genome.
total4,630,707100.0%

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≤ 10000014687
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 ≤ 5000186
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.29634

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 input15:18:02 18 Oct 201615:27:48 18 Oct 20169 minutes 46 seconds
Read alignment to reference genome15:27:49 18 Oct 201617:04:28 18 Oct 20161 hour 36 minutes 39 seconds
Preprocessing alignments for candidate junction identification17:04:28 18 Oct 201617:40:20 18 Oct 201635 minutes 52 seconds
Preliminary analysis of coverage distribution17:40:20 18 Oct 201618:15:23 18 Oct 201635 minutes 3 seconds
Identifying junction candidates18:15:23 18 Oct 201618:15:43 18 Oct 201620 seconds
Re-alignment to junction candidates18:15:43 18 Oct 201618:42:46 18 Oct 201627 minutes 3 seconds
Resolving alignments with junction candidates18:42:46 18 Oct 201619:41:19 18 Oct 201658 minutes 33 seconds
Creating BAM files19:41:19 18 Oct 201619:58:42 18 Oct 201617 minutes 23 seconds
Tabulating error counts19:58:42 18 Oct 201620:18:19 18 Oct 201619 minutes 37 seconds
Re-calibrating base error rates20:18:19 18 Oct 201620:18:22 18 Oct 20163 seconds
Examining read alignment evidence20:18:22 18 Oct 201622:17:12 18 Oct 20161 hour 58 minutes 50 seconds
Polymorphism statistics22:17:12 18 Oct 201622:17:14 18 Oct 20162 seconds
Output22:17:14 18 Oct 201622:19:00 18 Oct 20161 minute 46 seconds
Total 7 hours 57 seconds