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-IL9_S13_L003_R1_0011,896,915285,571,35699.8%150.5 bases151 bases99.0%
errorsALE-IL9_S13_L003_R2_0011,894,509285,179,44499.6%150.5 bases151 bases96.9%
errorsALE-IL9_S13_L001_R2_0011,873,562282,017,58199.5%150.5 bases151 bases97.2%
errorsALE-IL9_S13_L001_R1_0011,873,673282,044,48799.6%150.5 bases151 bases99.2%
errorsALE-IL9_S13_L002_R2_0011,870,323281,540,08099.6%150.5 bases151 bases97.3%
errorsALE-IL9_S13_L002_R1_0011,871,194281,682,23799.6%150.5 bases151 bases99.2%
errorsALE-IL9_S13_L004_R1_0011,903,474286,574,04399.8%150.6 bases151 bases99.2%
errorsALE-IL9_S13_L004_R2_0011,899,890286,015,52299.6%150.5 bases151 bases97.6%
total15,083,5402,270,624,75099.6%150.5 bases151 bases98.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652480.33.9100.0%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≤ 1000004300
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 ≤ 5000156
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.010

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.30895

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 input10:46:32 21 Apr 201610:52:42 21 Apr 20166 minutes 10 seconds
Read alignment to reference genome10:52:43 21 Apr 201611:08:33 21 Apr 201615 minutes 50 seconds
Preprocessing alignments for candidate junction identification11:08:33 21 Apr 201611:15:46 21 Apr 20167 minutes 13 seconds
Preliminary analysis of coverage distribution11:15:46 21 Apr 201611:32:15 21 Apr 201616 minutes 29 seconds
Identifying junction candidates11:32:15 21 Apr 201611:32:17 21 Apr 20162 seconds
Re-alignment to junction candidates11:32:17 21 Apr 201611:35:29 21 Apr 20163 minutes 12 seconds
Resolving alignments with junction candidates11:35:29 21 Apr 201611:52:36 21 Apr 201617 minutes 7 seconds
Creating BAM files11:52:36 21 Apr 201612:03:05 21 Apr 201610 minutes 29 seconds
Tabulating error counts12:03:05 21 Apr 201612:22:59 21 Apr 201619 minutes 54 seconds
Re-calibrating base error rates12:22:59 21 Apr 201612:23:08 21 Apr 20169 seconds
Examining read alignment evidence12:23:08 21 Apr 201614:41:47 21 Apr 20162 hours 18 minutes 39 seconds
Polymorphism statistics14:41:47 21 Apr 201614:41:50 21 Apr 20163 seconds
Output14:41:50 21 Apr 201614:44:22 21 Apr 20162 minutes 32 seconds
Total 3 hours 57 minutes 49 seconds