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-IL29_S37_L003_R1_0012,052,225308,953,88499.8%150.5 bases151 bases99.1%
errorsALE-IL29_S37_L004_R1_0012,030,622305,717,04399.7%150.6 bases151 bases99.2%
errorsALE-IL29_S37_L004_R2_0012,029,845305,578,18499.7%150.5 bases151 bases97.8%
errorsALE-IL29_S37_L002_R1_0012,017,085303,647,38799.5%150.5 bases151 bases99.3%
errorsALE-IL29_S37_L001_R1_0012,033,143306,050,50999.5%150.5 bases151 bases99.3%
errorsALE-IL29_S37_L002_R2_0012,018,736303,882,77199.6%150.5 bases151 bases97.5%
errorsALE-IL29_S37_L001_R2_0012,035,253306,355,17099.6%150.5 bases151 bases97.5%
errorsALE-IL29_S37_L003_R2_0012,051,740308,846,46299.7%150.5 bases151 bases97.2%
total16,268,6492,449,031,41099.7%150.5 bases151 bases98.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652517.012.4100.0%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≤ 10000035231
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 ≤ 5000247
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.016

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.29089

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 input17:54:57 22 Apr 201618:01:50 22 Apr 20166 minutes 53 seconds
Read alignment to reference genome18:01:50 22 Apr 201618:16:40 22 Apr 201614 minutes 50 seconds
Preprocessing alignments for candidate junction identification18:16:40 22 Apr 201618:23:23 22 Apr 20166 minutes 43 seconds
Preliminary analysis of coverage distribution18:23:23 22 Apr 201618:40:00 22 Apr 201616 minutes 37 seconds
Identifying junction candidates18:40:00 22 Apr 201618:40:06 22 Apr 20166 seconds
Re-alignment to junction candidates18:40:06 22 Apr 201618:43:18 22 Apr 20163 minutes 12 seconds
Resolving alignments with junction candidates18:43:18 22 Apr 201619:03:51 22 Apr 201620 minutes 33 seconds
Creating BAM files19:03:51 22 Apr 201619:14:43 22 Apr 201610 minutes 52 seconds
Tabulating error counts19:14:43 22 Apr 201619:27:59 22 Apr 201613 minutes 16 seconds
Re-calibrating base error rates19:27:59 22 Apr 201619:28:01 22 Apr 20162 seconds
Examining read alignment evidence19:28:01 22 Apr 201621:40:03 22 Apr 20162 hours 12 minutes 2 seconds
Polymorphism statistics21:40:03 22 Apr 201621:40:05 22 Apr 20162 seconds
Output21:40:05 22 Apr 201621:42:05 22 Apr 20162 minutes 0 seconds
Total 3 hours 47 minutes 8 seconds