breseq  version 0.26.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-NXT-Ace2_S6_L001_R1_001_10112015764,577105,860,29599.9%138.5 bases141 bases99.7%
errorsSSW-NXT-Ace2_S6_L001_R2_001_10252015954,513140,128,75499.9%146.8 bases150 bases99.2%
errorsSSW-NXT-Ace2_S6_L001_R2_001_10112015764,55399,325,06999.9%129.9 bases132 bases99.0%
errorsSSW-NXT-Ace2_S6_L001_R1_001_10252015954,585183,824,89799.9%192.6 bases200 bases99.7%
total3,438,228529,139,01599.9%153.9 bases200 bases99.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652117.83.5100.0%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≤ 1000005258
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 ≤ 5000152
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.013

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.77533

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
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.1
Polymorphism minimum coverage each strand2
Polymorphism bias cutoff0.05
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 input00:17:05 28 Oct 201500:18:02 28 Oct 201557 seconds
Read alignment to reference genome00:18:03 28 Oct 201500:21:43 28 Oct 20153 minutes 40 seconds
Preprocessing alignments for candidate junction identification00:21:43 28 Oct 201500:23:10 28 Oct 20151 minute 27 seconds
Preliminary analysis of coverage distribution00:23:10 28 Oct 201500:26:14 28 Oct 20153 minutes 4 seconds
Identifying junction candidates00:26:14 28 Oct 201500:26:15 28 Oct 20151 second
Re-alignment to junction candidates00:26:15 28 Oct 201500:26:59 28 Oct 201544 seconds
Resolving alignments with junction candidates00:26:59 28 Oct 201500:29:27 28 Oct 20152 minutes 28 seconds
Creating BAM files00:29:27 28 Oct 201500:31:23 28 Oct 20151 minute 56 seconds
Tabulating error counts00:31:23 28 Oct 201500:34:55 28 Oct 20153 minutes 32 seconds
Re-calibrating base error rates00:34:55 28 Oct 201500:34:58 28 Oct 20153 seconds
Examining read alignment evidence00:34:58 28 Oct 201501:03:10 28 Oct 201528 minutes 12 seconds
Polymorphism statistics01:03:10 28 Oct 201501:03:11 28 Oct 20151 second
Output01:03:11 28 Oct 201501:04:57 28 Oct 20151 minute 46 seconds
Total 47 minutes 51 seconds