breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorspgi-7_S5_L001_R1_0011,046,130296,416,322100.0%283.3 bases301 bases99.1%
errorspgi-7_S5_L001_R2_0011,046,068220,575,511100.0%210.9 bases218 bases98.3%
total2,092,198516,991,833100.0%247.1 bases301 bases98.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652116.44.1100.0%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≤ 1000002030
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 ≤ 500079
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_0009130.86259

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 input19:27:31 17 Jun 201619:28:14 17 Jun 201643 seconds
Read alignment to reference genome19:28:15 17 Jun 201619:31:06 17 Jun 20162 minutes 51 seconds
Preprocessing alignments for candidate junction identification19:31:06 17 Jun 201619:32:04 17 Jun 201658 seconds
Preliminary analysis of coverage distribution19:32:04 17 Jun 201619:34:57 17 Jun 20162 minutes 53 seconds
Identifying junction candidates19:34:57 17 Jun 201619:34:57 17 Jun 20160 seconds
Re-alignment to junction candidates19:34:57 17 Jun 201619:35:22 17 Jun 201625 seconds
Resolving alignments with junction candidates19:35:22 17 Jun 201619:37:36 17 Jun 20162 minutes 14 seconds
Creating BAM files19:37:36 17 Jun 201619:39:21 17 Jun 20161 minute 45 seconds
Tabulating error counts19:39:21 17 Jun 201619:42:10 17 Jun 20162 minutes 49 seconds
Re-calibrating base error rates19:42:10 17 Jun 201619:42:11 17 Jun 20161 second
Examining read alignment evidence19:42:11 17 Jun 201620:02:18 17 Jun 201620 minutes 7 seconds
Polymorphism statistics20:02:18 17 Jun 201620:02:19 17 Jun 20161 second
Output20:02:19 17 Jun 201620:03:18 17 Jun 201659 seconds
Total 35 minutes 46 seconds