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-IL39_S47_L001_R1_0011,685,208253,650,28999.7%150.5 bases151 bases99.5%
errorsALE-IL39_S47_L001_R2_0011,683,932253,446,43499.7%150.5 bases151 bases98.0%
errorsALE-IL39_S47_L002_R1_0011,674,753252,090,21799.8%150.5 bases151 bases99.5%
errorsALE-IL39_S47_L002_R2_0011,672,760251,781,34599.7%150.5 bases151 bases98.1%
errorsALE-IL39_S47_L003_R1_0011,700,267255,940,11599.9%150.5 bases151 bases99.3%
errorsALE-IL39_S47_L003_R2_0011,698,609255,663,31499.8%150.5 bases151 bases97.8%
errorsALE-IL39_S47_L004_R1_0011,694,683255,114,34199.9%150.5 bases151 bases99.4%
errorsALE-IL39_S47_L004_R2_0011,692,540254,770,00399.7%150.5 bases151 bases98.2%
total13,502,7522,032,456,05899.8%150.5 bases151 bases98.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionDH14,630,707435.53.698.2%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≤ 10000014745
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 ≤ 5000296
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.020

Junction Skew Score Calculation

reference sequencepr(no read start)
DH10.34027

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 input22:20:20 18 Oct 201622:34:35 18 Oct 201614 minutes 15 seconds
Read alignment to reference genome22:34:51 18 Oct 201600:04:01 19 Oct 20161 hour 29 minutes 10 seconds
Preprocessing alignments for candidate junction identification00:04:01 19 Oct 201600:12:54 19 Oct 20168 minutes 53 seconds
Preliminary analysis of coverage distribution00:12:54 19 Oct 201601:07:33 19 Oct 201654 minutes 39 seconds
Identifying junction candidates01:07:33 19 Oct 201601:09:22 19 Oct 20161 minute 49 seconds
Re-alignment to junction candidates01:09:22 19 Oct 201602:08:58 19 Oct 201659 minutes 36 seconds
Resolving alignments with junction candidates02:08:58 19 Oct 201603:25:25 19 Oct 20161 hour 16 minutes 27 seconds
Creating BAM files03:25:25 19 Oct 201603:52:21 19 Oct 201626 minutes 56 seconds
Tabulating error counts03:52:21 19 Oct 201604:06:56 19 Oct 201614 minutes 35 seconds
Re-calibrating base error rates04:06:56 19 Oct 201604:06:59 19 Oct 20163 seconds
Examining read alignment evidence04:06:59 19 Oct 201606:23:20 19 Oct 20162 hours 16 minutes 21 seconds
Polymorphism statistics06:23:20 19 Oct 201606:23:23 19 Oct 20163 seconds
Output06:23:23 19 Oct 201606:26:05 19 Oct 20162 minutes 42 seconds
Total 8 hours 5 minutes 29 seconds