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_A4_F053_I0_R1_S22_L004_R1_0013,255,691325,198,041100.0%99.9 bases100 bases97.2%
errorsqtrim-IND_KHP_HOT_A4_F053_I0_R1_S22_L004_R2_0013,255,663324,864,651100.0%99.8 bases100 bases96.3%
total6,511,354650,062,692100.0%99.8 bases100 bases96.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652135.32.498.1%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≤ 100000100091
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 ≤ 50002203
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.099

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.56133

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 input13:25:58 11 Jan 201713:27:06 11 Jan 20171 minute 8 seconds
Read alignment to reference genome13:27:07 11 Jan 201713:31:17 11 Jan 20174 minutes 10 seconds
Preprocessing alignments for candidate junction identification13:31:17 11 Jan 201713:33:39 11 Jan 20172 minutes 22 seconds
Preliminary analysis of coverage distribution13:33:39 11 Jan 201713:36:24 11 Jan 20172 minutes 45 seconds
Identifying junction candidates13:36:24 11 Jan 201714:17:23 11 Jan 201740 minutes 59 seconds
Re-alignment to junction candidates14:17:23 11 Jan 201714:18:37 11 Jan 20171 minute 14 seconds
Resolving alignments with junction candidates14:18:37 11 Jan 201714:23:13 11 Jan 20174 minutes 36 seconds
Creating BAM files14:23:13 11 Jan 201714:24:55 11 Jan 20171 minute 42 seconds
Tabulating error counts14:24:55 11 Jan 201714:27:48 11 Jan 20172 minutes 53 seconds
Re-calibrating base error rates14:27:48 11 Jan 201714:27:48 11 Jan 20170 seconds
Examining read alignment evidence14:27:48 11 Jan 201715:48:50 11 Jan 20171 hour 21 minutes 2 seconds
Polymorphism statistics15:48:50 11 Jan 201715:48:53 11 Jan 20173 seconds
Output15:48:53 11 Jan 201715:51:26 11 Jan 20172 minutes 33 seconds
Total 2 hours 25 minutes 27 seconds