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_A11_F212_I0_R1_S55_L004_R1_0013,048,825304,511,513100.0%99.9 bases100 bases93.7%
errorsqtrim-IND_KHP_HOT_A11_F212_I0_R1_S55_L004_R2_0013,048,791303,792,953100.0%99.6 bases100 bases92.5%
total6,097,616608,304,466100.0%99.8 bases100 bases93.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652122.02.698.1%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≤ 100000100004
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 ≤ 50001520
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.068

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.59593

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoffOFF
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.15
Polymorphism minimum coverage each strand2
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥2 bases

Execution Times

stepstartendelapsed
Read and reference sequence file input23:42:51 12 Jan 201723:43:53 12 Jan 20171 minute 2 seconds
Read alignment to reference genome23:43:54 12 Jan 201723:47:33 12 Jan 20173 minutes 39 seconds
Preprocessing alignments for candidate junction identification23:47:33 12 Jan 201723:49:47 12 Jan 20172 minutes 14 seconds
Preliminary analysis of coverage distribution23:49:47 12 Jan 201723:52:23 12 Jan 20172 minutes 36 seconds
Identifying junction candidates23:52:23 12 Jan 201700:06:58 13 Jan 201714 minutes 35 seconds
Re-alignment to junction candidates00:06:58 13 Jan 201700:07:45 13 Jan 201747 seconds
Resolving alignments with junction candidates00:07:45 13 Jan 201700:11:17 13 Jan 20173 minutes 32 seconds
Creating BAM files00:11:17 13 Jan 201700:12:55 13 Jan 20171 minute 38 seconds
Tabulating error counts00:12:55 13 Jan 201700:15:28 13 Jan 20172 minutes 33 seconds
Re-calibrating base error rates00:15:28 13 Jan 201700:15:28 13 Jan 20170 seconds
Examining read alignment evidence00:15:28 13 Jan 201701:49:17 13 Jan 20171 hour 33 minutes 49 seconds
Polymorphism statistics01:49:17 13 Jan 201701:49:22 13 Jan 20175 seconds
Output01:49:22 13 Jan 201701:51:44 13 Jan 20172 minutes 22 seconds
Total 2 hours 8 minutes 52 seconds