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_A8_F232_I0_R1_S75_L004_R1_0013,823,244382,184,596100.0%100.0 bases100 bases94.5%
errorsqtrim-IND_KHP_HOT_A8_F232_I0_R1_S75_L004_R2_0013,823,216381,103,086100.0%99.7 bases100 bases93.1%
total7,646,460763,287,682100.0%99.8 bases100 bases93.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652156.36.698.0%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≤ 100000100018
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000613
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.027

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.52724

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 input22:19:51 13 Jan 201722:21:14 13 Jan 20171 minute 23 seconds
Read alignment to reference genome22:21:15 13 Jan 201722:25:53 13 Jan 20174 minutes 38 seconds
Preprocessing alignments for candidate junction identification22:25:53 13 Jan 201722:28:45 13 Jan 20172 minutes 52 seconds
Preliminary analysis of coverage distribution22:28:45 13 Jan 201722:31:51 13 Jan 20173 minutes 6 seconds
Identifying junction candidates22:31:51 13 Jan 201722:34:00 13 Jan 20172 minutes 9 seconds
Re-alignment to junction candidates22:34:00 13 Jan 201722:34:53 13 Jan 201753 seconds
Resolving alignments with junction candidates22:34:53 13 Jan 201722:40:17 13 Jan 20175 minutes 24 seconds
Creating BAM files22:40:17 13 Jan 201722:42:58 13 Jan 20172 minutes 41 seconds
Tabulating error counts22:42:58 13 Jan 201722:46:18 13 Jan 20173 minutes 20 seconds
Re-calibrating base error rates22:46:18 13 Jan 201722:46:19 13 Jan 20171 second
Examining read alignment evidence22:46:19 13 Jan 201700:28:16 14 Jan 20171 hour 41 minutes 57 seconds
Polymorphism statistics00:28:16 14 Jan 201700:28:23 14 Jan 20177 seconds
Output00:28:23 14 Jan 201700:30:14 14 Jan 20171 minute 51 seconds
Total 2 hours 10 minutes 22 seconds