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-IL28_S36_L002_R1_0012,175,287327,483,77099.7%150.5 bases151 bases99.5%
errorsALE-IL28_S36_L003_R1_0012,213,457333,241,40699.8%150.6 bases151 bases99.3%
errorsALE-IL28_S36_L002_R2_0012,174,030327,286,90199.6%150.5 bases151 bases98.0%
errorsALE-IL28_S36_L001_R2_0012,192,553330,062,24599.6%150.5 bases151 bases97.9%
errorsALE-IL28_S36_L003_R2_0012,211,338332,889,95099.7%150.5 bases151 bases97.6%
errorsALE-IL28_S36_L004_R1_0012,186,201329,158,35799.8%150.6 bases151 bases99.4%
errorsALE-IL28_S36_L004_R2_0012,183,515328,731,97399.7%150.6 bases151 bases98.1%
errorsALE-IL28_S36_L001_R1_0012,193,630330,229,45699.7%150.5 bases151 bases99.5%
total17,530,0112,639,084,05899.7%150.5 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652562.011.6100.0%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≤ 10000036906
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 ≤ 5000218
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.014

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.27070

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 input12:55:37 22 Apr 201613:02:32 22 Apr 20166 minutes 55 seconds
Read alignment to reference genome13:02:32 22 Apr 201613:20:38 22 Apr 201618 minutes 6 seconds
Preprocessing alignments for candidate junction identification13:20:38 22 Apr 201613:31:00 22 Apr 201610 minutes 22 seconds
Preliminary analysis of coverage distribution13:31:00 22 Apr 201613:54:31 22 Apr 201623 minutes 31 seconds
Identifying junction candidates13:54:31 22 Apr 201613:55:41 22 Apr 20161 minute 10 seconds
Re-alignment to junction candidates13:55:41 22 Apr 201614:16:07 22 Apr 201620 minutes 26 seconds
Resolving alignments with junction candidates14:16:07 22 Apr 201615:07:25 22 Apr 201651 minutes 18 seconds
Creating BAM files15:07:25 22 Apr 201615:21:39 22 Apr 201614 minutes 14 seconds
Tabulating error counts15:21:39 22 Apr 201615:42:13 22 Apr 201620 minutes 34 seconds
Re-calibrating base error rates15:42:13 22 Apr 201615:42:17 22 Apr 20164 seconds
Examining read alignment evidence15:42:17 22 Apr 201617:50:57 22 Apr 20162 hours 8 minutes 40 seconds
Polymorphism statistics17:50:57 22 Apr 201617:51:03 22 Apr 20166 seconds
Output17:51:03 22 Apr 201617:54:57 22 Apr 20163 minutes 54 seconds
Total 4 hours 59 minutes 20 seconds