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-IL3_S3_L002_R1_0011,820,622274,017,21699.2%150.5 bases151 bases98.6%
errorsALE-IL3_S3_L002_R2_0011,826,865274,948,96899.5%150.5 bases151 bases95.3%
errorsALE-IL3_S3_L003_R1_0011,852,220278,783,10599.5%150.5 bases151 bases98.1%
errorsALE-IL3_S3_L004_R2_0011,835,694276,287,90099.5%150.5 bases151 bases95.7%
errorsALE-IL3_S3_L001_R2_0011,835,680276,262,74099.5%150.5 bases151 bases95.3%
errorsALE-IL3_S3_L001_R1_0011,828,414275,171,46699.1%150.5 bases151 bases98.6%
errorsALE-IL3_S3_L003_R2_0011,853,773278,989,32499.6%150.5 bases151 bases95.0%
errorsALE-IL3_S3_L004_R1_0011,835,258276,240,74799.5%150.5 bases151 bases98.5%
total14,688,5262,210,701,46699.4%150.5 bases151 bases96.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652458.93.8100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.

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

Number of alignment pairs examined for constructing junction candidates≤ 10000010434
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 ≤ 5000244
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.016

Junction Skew Score Calculation

reference sequencepr(no read start)

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

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

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

Read and reference sequence file input10:07:26 22 Apr 201610:13:27 22 Apr 20166 minutes 1 second
Read alignment to reference genome10:13:27 22 Apr 201610:24:45 22 Apr 201611 minutes 18 seconds
Preprocessing alignments for candidate junction identification10:24:45 22 Apr 201610:30:45 22 Apr 20166 minutes 0 seconds
Preliminary analysis of coverage distribution10:30:45 22 Apr 201610:47:11 22 Apr 201616 minutes 26 seconds
Identifying junction candidates10:47:11 22 Apr 201610:47:13 22 Apr 20162 seconds
Re-alignment to junction candidates10:47:13 22 Apr 201610:50:17 22 Apr 20163 minutes 4 seconds
Resolving alignments with junction candidates10:50:17 22 Apr 201611:05:20 22 Apr 201615 minutes 3 seconds
Creating BAM files11:05:20 22 Apr 201611:15:43 22 Apr 201610 minutes 23 seconds
Tabulating error counts11:15:43 22 Apr 201611:33:05 22 Apr 201617 minutes 22 seconds
Re-calibrating base error rates11:33:06 22 Apr 201611:33:08 22 Apr 20162 seconds
Examining read alignment evidence11:33:08 22 Apr 201613:24:18 22 Apr 20161 hour 51 minutes 10 seconds
Polymorphism statistics13:24:18 22 Apr 201613:24:23 22 Apr 20165 seconds
Output13:24:23 22 Apr 201613:27:11 22 Apr 20162 minutes 48 seconds
Total 3 hours 19 minutes 44 seconds