breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL2_S2_L003_R1_0011,857,193279,549,31099.4%150.5 bases151 bases96.1%
errorsALE-IL2_S2_L004_R2_0011,854,170279,097,68799.6%150.5 bases151 bases94.0%
errorsALE-IL2_S2_L003_R2_0011,860,657280,043,72799.6%150.5 bases151 bases93.1%
errorsALE-IL2_S2_L001_R2_0011,846,112277,850,92499.5%150.5 bases151 bases93.4%
errorsALE-IL2_S2_L004_R1_0011,852,979278,936,47599.5%150.5 bases151 bases96.6%
errorsALE-IL2_S2_L001_R1_0011,836,116276,348,04399.0%150.5 bases151 bases96.6%
errorsALE-IL2_S2_L002_R1_0011,829,020275,302,57199.0%150.5 bases151 bases96.6%
errorsALE-IL2_S2_L002_R2_0011,837,742276,611,36899.5%150.5 bases151 bases93.5%
total14,773,9892,223,740,10599.4%150.5 bases151 bases95.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652455.04.4100.0%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≤ 10000010272
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 ≤ 5000182
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.32367

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 input13:27:18 22 Apr 201613:34:02 22 Apr 20166 minutes 44 seconds
Read alignment to reference genome13:34:03 22 Apr 201613:49:05 22 Apr 201615 minutes 2 seconds
Preprocessing alignments for candidate junction identification13:49:05 22 Apr 201613:56:26 22 Apr 20167 minutes 21 seconds
Preliminary analysis of coverage distribution13:56:26 22 Apr 201614:22:51 22 Apr 201626 minutes 25 seconds
Identifying junction candidates14:22:51 22 Apr 201614:22:52 22 Apr 20161 second
Re-alignment to junction candidates14:22:52 22 Apr 201614:37:04 22 Apr 201614 minutes 12 seconds
Resolving alignments with junction candidates14:37:04 22 Apr 201615:06:23 22 Apr 201629 minutes 19 seconds
Creating BAM files15:06:23 22 Apr 201615:17:35 22 Apr 201611 minutes 12 seconds
Tabulating error counts15:17:35 22 Apr 201615:34:54 22 Apr 201617 minutes 19 seconds
Re-calibrating base error rates15:34:54 22 Apr 201615:34:57 22 Apr 20163 seconds
Examining read alignment evidence15:34:57 22 Apr 201617:21:42 22 Apr 20161 hour 46 minutes 45 seconds
Polymorphism statistics17:21:42 22 Apr 201617:21:46 22 Apr 20164 seconds
Output17:21:46 22 Apr 201617:24:47 22 Apr 20163 minutes 1 second
Total 3 hours 57 minutes 28 seconds