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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-KHP-SSW-3-164-3-1_S1_L001_R1_001370,249102,579,070100.0%277.1 bases301 bases98.1%
errorsSSW-KHP-SSW-3-164-3-1_S13_L001_R2_001184,39655,379,78899.9%300.3 bases301 bases71.8%
errorsSSW-KHP-SSW-3-164-3-1_S1_L001_R2_001370,236103,150,398100.0%278.6 bases301 bases95.1%
errorsSSW-KHP-SSW-3-164-3-1_S13_L001_R1_001184,62655,493,537100.0%300.6 bases301 bases73.6%
total1,109,507316,602,793100.0%285.4 bases301 bases88.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65259.82.0100.0%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≤ 1000007374
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500016
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.91248

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 input13:30:36 21 Mar 201613:31:10 21 Mar 201634 seconds
Read alignment to reference genome13:31:10 21 Mar 201613:33:26 21 Mar 20162 minutes 16 seconds
Preprocessing alignments for candidate junction identification13:33:26 21 Mar 201613:33:58 21 Mar 201632 seconds
Preliminary analysis of coverage distribution13:33:58 21 Mar 201613:35:27 21 Mar 20161 minute 29 seconds
Identifying junction candidates13:35:27 21 Mar 201613:35:28 21 Mar 20161 second
Re-alignment to junction candidates13:35:28 21 Mar 201613:35:42 21 Mar 201614 seconds
Resolving alignments with junction candidates13:35:42 21 Mar 201613:36:52 21 Mar 20161 minute 10 seconds
Creating BAM files13:36:52 21 Mar 201613:37:44 21 Mar 201652 seconds
Tabulating error counts13:37:44 21 Mar 201613:39:16 21 Mar 20161 minute 32 seconds
Re-calibrating base error rates13:39:16 21 Mar 201613:39:17 21 Mar 20161 second
Examining read alignment evidence13:39:17 21 Mar 201613:50:29 21 Mar 201611 minutes 12 seconds
Polymorphism statistics13:50:29 21 Mar 201613:50:30 21 Mar 20161 second
Output13:50:30 21 Mar 201613:50:50 21 Mar 201620 seconds
Total 20 minutes 14 seconds