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-IL23_S31_L003_R2_0011,831,458275,672,77199.8%150.5 bases151 bases97.7%
errorsALE-IL23_S31_L004_R1_0011,834,280276,150,56799.9%150.5 bases151 bases99.5%
errorsALE-IL23_S31_L001_R1_0011,812,533272,831,74799.8%150.5 bases151 bases99.5%
errorsALE-IL23_S31_L004_R2_0011,830,863275,614,50399.7%150.5 bases151 bases98.3%
errorsALE-IL23_S31_L001_R2_0011,809,563272,375,44699.7%150.5 bases151 bases98.1%
errorsALE-IL23_S31_L002_R2_0011,799,760270,916,10599.6%150.5 bases151 bases98.1%
errorsALE-IL23_S31_L003_R1_0011,833,829276,060,41999.9%150.5 bases151 bases99.4%
errorsALE-IL23_S31_L002_R1_0011,803,210271,450,36699.8%150.5 bases151 bases99.5%
total14,555,4962,191,071,92499.8%150.5 bases151 bases98.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652466.16.2100.0%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≤ 10000012273
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 ≤ 5000240
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.016

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.31450

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 input03:55:03 21 Apr 201604:01:08 21 Apr 20166 minutes 5 seconds
Read alignment to reference genome04:01:09 21 Apr 201604:17:46 21 Apr 201616 minutes 37 seconds
Preprocessing alignments for candidate junction identification04:17:47 21 Apr 201604:29:16 21 Apr 201611 minutes 29 seconds
Preliminary analysis of coverage distribution04:29:16 21 Apr 201604:51:05 21 Apr 201621 minutes 49 seconds
Identifying junction candidates04:51:05 21 Apr 201604:51:10 21 Apr 20165 seconds
Re-alignment to junction candidates04:51:10 21 Apr 201604:59:25 21 Apr 20168 minutes 15 seconds
Resolving alignments with junction candidates04:59:25 21 Apr 201605:26:37 21 Apr 201627 minutes 12 seconds
Creating BAM files05:26:37 21 Apr 201605:38:58 21 Apr 201612 minutes 21 seconds
Tabulating error counts05:38:58 21 Apr 201605:54:38 21 Apr 201615 minutes 40 seconds
Re-calibrating base error rates05:54:38 21 Apr 201605:54:42 21 Apr 20164 seconds
Examining read alignment evidence05:54:42 21 Apr 201608:00:54 21 Apr 20162 hours 6 minutes 12 seconds
Polymorphism statistics08:00:54 21 Apr 201608:00:56 21 Apr 20162 seconds
Output08:00:56 21 Apr 201608:03:43 21 Apr 20162 minutes 47 seconds
Total 4 hours 8 minutes 38 seconds