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_I1_R1_S48_L004_R2_0011,946,099194,279,210100.0%99.8 bases100 bases96.5%
errorsqtrim-IND_KHP_HOT_A11_F212_I1_R1_S48_L004_R1_0011,946,112194,551,763100.0%100.0 bases100 bases96.9%
total3,892,211388,830,973100.0%99.9 bases100 bases96.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65280.01.998.1%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≤ 10000074880
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 ≤ 50001126
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_0009130.69626

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 input20:08:23 04 Jan 201720:09:04 04 Jan 201741 seconds
Read alignment to reference genome20:09:05 04 Jan 201720:11:16 04 Jan 20172 minutes 11 seconds
Preprocessing alignments for candidate junction identification20:11:16 04 Jan 201720:12:40 04 Jan 20171 minute 24 seconds
Preliminary analysis of coverage distribution20:12:40 04 Jan 201720:14:12 04 Jan 20171 minute 32 seconds
Identifying junction candidates20:14:12 04 Jan 201720:22:28 04 Jan 20178 minutes 16 seconds
Re-alignment to junction candidates20:22:28 04 Jan 201720:22:56 04 Jan 201728 seconds
Resolving alignments with junction candidates20:22:56 04 Jan 201720:25:17 04 Jan 20172 minutes 21 seconds
Creating BAM files20:25:17 04 Jan 201720:26:11 04 Jan 201754 seconds
Tabulating error counts20:26:11 04 Jan 201720:27:51 04 Jan 20171 minute 40 seconds
Re-calibrating base error rates20:27:51 04 Jan 201720:27:51 04 Jan 20170 seconds
Examining read alignment evidence20:27:51 04 Jan 201720:40:26 04 Jan 201712 minutes 35 seconds
Polymorphism statistics20:40:26 04 Jan 201720:40:26 04 Jan 20170 seconds
Output20:40:26 04 Jan 201720:41:35 04 Jan 20171 minute 9 seconds
Total 33 minutes 11 seconds