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-7-90-3-1_S1_L001_R1_0012,592,334708,686,134100.0%273.4 bases301 bases95.3%
errorsSSW-KHP-SSW-7-90-3-1_S1_L001_R2_0012,591,557721,890,812100.0%278.6 bases301 bases82.0%
total5,183,8911,430,576,946100.0%276.0 bases301 bases88.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652267.52.8100.0%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≤ 10000027311
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 ≤ 5000175
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.023

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.69409

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 input19:12:28 16 Mar 201619:16:45 16 Mar 20164 minutes 17 seconds
Read alignment to reference genome19:16:46 16 Mar 201619:31:01 16 Mar 201614 minutes 15 seconds
Preprocessing alignments for candidate junction identification19:31:01 16 Mar 201619:34:05 16 Mar 20163 minutes 4 seconds
Preliminary analysis of coverage distribution19:34:05 16 Mar 201619:41:31 16 Mar 20167 minutes 26 seconds
Identifying junction candidates19:41:31 16 Mar 201619:41:38 16 Mar 20167 seconds
Re-alignment to junction candidates19:41:38 16 Mar 201619:43:07 16 Mar 20161 minute 29 seconds
Resolving alignments with junction candidates19:43:07 16 Mar 201619:51:33 16 Mar 20168 minutes 26 seconds
Creating BAM files19:51:33 16 Mar 201619:56:03 16 Mar 20164 minutes 30 seconds
Tabulating error counts19:56:03 16 Mar 201620:06:24 16 Mar 201610 minutes 21 seconds
Re-calibrating base error rates20:06:24 16 Mar 201620:06:26 16 Mar 20162 seconds
Examining read alignment evidence20:06:26 16 Mar 201621:20:57 16 Mar 20161 hour 14 minutes 31 seconds
Polymorphism statistics21:20:57 16 Mar 201621:20:58 16 Mar 20161 second
Output21:20:58 16 Mar 201621:22:28 16 Mar 20161 minute 30 seconds
Total 2 hours 9 minutes 59 seconds