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-IL19_S27_L001_R1_0012,232,806336,108,05999.7%150.5 bases151 bases99.2%
errorsALE-IL19_S27_L001_R2_0012,232,326336,020,78199.7%150.5 bases151 bases97.7%
errorsALE-IL19_S27_L002_R1_0012,218,455333,965,98699.7%150.5 bases151 bases99.2%
errorsALE-IL19_S27_L002_R2_0012,217,498333,808,00699.7%150.5 bases151 bases97.7%
errorsALE-IL19_S27_L003_R1_0012,257,233339,815,47099.8%150.5 bases151 bases99.0%
errorsALE-IL19_S27_L003_R2_0012,255,699339,543,90099.8%150.5 bases151 bases97.4%
errorsALE-IL19_S27_L004_R1_0012,250,543338,826,05399.8%150.6 bases151 bases99.1%
errorsALE-IL19_S27_L004_R2_0012,248,317338,462,25499.7%150.5 bases151 bases97.9%
total17,912,8772,696,550,50999.7%150.5 bases151 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707570.53.898.2%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≤ 10000014291
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 ≤ 5000174
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.26075

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 input15:17:45 18 Oct 201615:27:49 18 Oct 201610 minutes 4 seconds
Read alignment to reference genome15:27:50 18 Oct 201617:25:32 18 Oct 20161 hour 57 minutes 42 seconds
Preprocessing alignments for candidate junction identification17:25:32 18 Oct 201617:57:57 18 Oct 201632 minutes 25 seconds
Preliminary analysis of coverage distribution17:57:57 18 Oct 201618:43:20 18 Oct 201645 minutes 23 seconds
Identifying junction candidates18:43:20 18 Oct 201618:44:01 18 Oct 201641 seconds
Re-alignment to junction candidates18:44:01 18 Oct 201619:14:50 18 Oct 201630 minutes 49 seconds
Resolving alignments with junction candidates19:14:50 18 Oct 201619:59:55 18 Oct 201645 minutes 5 seconds
Creating BAM files19:59:55 18 Oct 201620:14:36 18 Oct 201614 minutes 41 seconds
Tabulating error counts20:14:36 18 Oct 201620:36:25 18 Oct 201621 minutes 49 seconds
Re-calibrating base error rates20:36:25 18 Oct 201620:36:27 18 Oct 20162 seconds
Examining read alignment evidence20:36:27 18 Oct 201623:05:28 18 Oct 20162 hours 29 minutes 1 second
Polymorphism statistics23:05:28 18 Oct 201623:05:35 18 Oct 20167 seconds
Output23:05:35 18 Oct 201623:10:44 18 Oct 20165 minutes 9 seconds
Total 7 hours 52 minutes 58 seconds