breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-IND_KHP_HOT_A3_F181_I1_R1_S14_L004_R1_0012,990,915299,002,289100.0%100.0 bases100 bases95.3%
errorsqtrim-IND_KHP_HOT_A3_F181_I1_R1_S14_L004_R2_0012,990,899298,673,756100.0%99.9 bases100 bases94.5%
total5,981,814597,676,045100.0%99.9 bases100 bases94.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652119.22.898.1%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≤ 10000028784
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 ≤ 50001113
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.050

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.59337

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 input15:28:01 04 Jan 201715:29:03 04 Jan 20171 minute 2 seconds
Read alignment to reference genome15:29:04 04 Jan 201715:32:28 04 Jan 20173 minutes 24 seconds
Preprocessing alignments for candidate junction identification15:32:28 04 Jan 201715:34:32 04 Jan 20172 minutes 4 seconds
Preliminary analysis of coverage distribution15:34:32 04 Jan 201715:36:49 04 Jan 20172 minutes 17 seconds
Identifying junction candidates15:36:49 04 Jan 201715:37:05 04 Jan 201716 seconds
Re-alignment to junction candidates15:37:05 04 Jan 201715:37:49 04 Jan 201744 seconds
Resolving alignments with junction candidates15:37:49 04 Jan 201715:41:19 04 Jan 20173 minutes 30 seconds
Creating BAM files15:41:19 04 Jan 201715:42:39 04 Jan 20171 minute 20 seconds
Tabulating error counts15:42:39 04 Jan 201715:45:13 04 Jan 20172 minutes 34 seconds
Re-calibrating base error rates15:45:13 04 Jan 201715:45:13 04 Jan 20170 seconds
Examining read alignment evidence15:45:13 04 Jan 201716:03:38 04 Jan 201718 minutes 25 seconds
Polymorphism statistics16:03:38 04 Jan 201716:03:38 04 Jan 20170 seconds
Output16:03:38 04 Jan 201716:04:19 04 Jan 201741 seconds
Total 36 minutes 17 seconds