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-IL21_S29_L001_R1_0012,018,241303,786,83699.7%150.5 bases151 bases99.3%
errorsALE-IL21_S29_L001_R2_0012,016,587303,528,18399.7%150.5 bases151 bases97.6%
errorsALE-IL21_S29_L002_R1_0012,003,917301,652,48799.8%150.5 bases151 bases99.2%
errorsALE-IL21_S29_L002_R2_0012,002,180301,373,54499.7%150.5 bases151 bases97.7%
errorsALE-IL21_S29_L003_R1_0012,042,131307,412,68499.9%150.5 bases151 bases99.1%
errorsALE-IL21_S29_L003_R2_0012,039,778307,020,08699.8%150.5 bases151 bases97.4%
errorsALE-IL21_S29_L004_R1_0012,034,549306,288,30699.9%150.5 bases151 bases99.2%
errorsALE-IL21_S29_L004_R2_0012,031,633305,824,83599.7%150.5 bases151 bases97.9%
total16,189,0162,436,886,96199.8%150.5 bases151 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707516.212.398.2%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≤ 10000012865
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 ≤ 5000180
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.28890

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 input15:18:21 18 Oct 201615:28:48 18 Oct 201610 minutes 27 seconds
Read alignment to reference genome15:28:49 18 Oct 201617:09:52 18 Oct 20161 hour 41 minutes 3 seconds
Preprocessing alignments for candidate junction identification17:09:52 18 Oct 201617:43:40 18 Oct 201633 minutes 48 seconds
Preliminary analysis of coverage distribution17:43:40 18 Oct 201618:17:30 18 Oct 201633 minutes 50 seconds
Identifying junction candidates18:17:30 18 Oct 201618:17:51 18 Oct 201621 seconds
Re-alignment to junction candidates18:17:51 18 Oct 201618:46:46 18 Oct 201628 minutes 55 seconds
Resolving alignments with junction candidates18:46:46 18 Oct 201619:46:36 18 Oct 201659 minutes 50 seconds
Creating BAM files19:46:36 18 Oct 201620:01:18 18 Oct 201614 minutes 42 seconds
Tabulating error counts20:01:18 18 Oct 201620:21:43 18 Oct 201620 minutes 25 seconds
Re-calibrating base error rates20:21:43 18 Oct 201620:21:46 18 Oct 20163 seconds
Examining read alignment evidence20:21:46 18 Oct 201622:23:36 18 Oct 20162 hours 1 minute 50 seconds
Polymorphism statistics22:23:36 18 Oct 201622:23:43 18 Oct 20167 seconds
Output22:23:43 18 Oct 201622:28:42 18 Oct 20164 minutes 59 seconds
Total 7 hours 10 minutes 20 seconds