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-IL30_S38_L004_R2_0011,769,201266,320,34699.7%150.5 bases151 bases97.7%
errorsALE-IL30_S38_L003_R1_0011,784,088268,561,66299.6%150.5 bases151 bases98.9%
errorsALE-IL30_S38_L001_R2_0011,769,618266,355,34899.7%150.5 bases151 bases97.3%
errorsALE-IL30_S38_L002_R1_0011,752,007263,725,52599.3%150.5 bases151 bases99.2%
errorsALE-IL30_S38_L001_R1_0011,762,611265,310,64399.3%150.5 bases151 bases99.2%
errorsALE-IL30_S38_L003_R2_0011,787,871269,103,89799.8%150.5 bases151 bases97.0%
errorsALE-IL30_S38_L004_R1_0011,766,267265,899,59299.6%150.5 bases151 bases99.1%
errorsALE-IL30_S38_L002_R2_0011,758,461264,689,98899.7%150.5 bases151 bases97.4%
total14,150,1242,129,967,00199.6%150.5 bases151 bases98.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652449.75.3100.0%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≤ 10000010802
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 ≤ 5000272
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.018

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.32231

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 input19:22:24 21 Apr 201619:28:08 21 Apr 20165 minutes 44 seconds
Read alignment to reference genome19:28:08 21 Apr 201619:42:53 21 Apr 201614 minutes 45 seconds
Preprocessing alignments for candidate junction identification19:42:53 21 Apr 201619:50:57 21 Apr 20168 minutes 4 seconds
Preliminary analysis of coverage distribution19:50:57 21 Apr 201620:12:13 21 Apr 201621 minutes 16 seconds
Identifying junction candidates20:12:13 21 Apr 201620:12:16 21 Apr 20163 seconds
Re-alignment to junction candidates20:12:16 21 Apr 201620:16:18 21 Apr 20164 minutes 2 seconds
Resolving alignments with junction candidates20:16:18 21 Apr 201620:37:53 21 Apr 201621 minutes 35 seconds
Creating BAM files20:37:53 21 Apr 201620:51:17 21 Apr 201613 minutes 24 seconds
Tabulating error counts20:51:18 21 Apr 201621:03:12 21 Apr 201611 minutes 54 seconds
Re-calibrating base error rates21:03:12 21 Apr 201621:03:17 21 Apr 20165 seconds
Examining read alignment evidence21:03:17 21 Apr 201622:46:49 21 Apr 20161 hour 43 minutes 32 seconds
Polymorphism statistics22:46:49 21 Apr 201622:46:52 21 Apr 20163 seconds
Output22:46:52 21 Apr 201622:49:20 21 Apr 20162 minutes 28 seconds
Total 3 hours 26 minutes 55 seconds