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_F120_I1_R1_S30_L004_R1_0012,694,360269,355,442100.0%100.0 bases100 bases95.2%
errorsqtrim-IND_KHP_HOT_A8_F120_I1_R1_S30_L004_R2_0012,694,332268,947,934100.0%99.8 bases100 bases94.7%
total5,388,692538,303,376100.0%99.9 bases100 bases95.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652109.71.798.1%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≤ 100000100000
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 ≤ 50001398
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.063

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.61827

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 input22:35:06 04 Jan 201722:36:01 04 Jan 201755 seconds
Read alignment to reference genome22:36:02 04 Jan 201722:39:11 04 Jan 20173 minutes 9 seconds
Preprocessing alignments for candidate junction identification22:39:11 04 Jan 201722:41:10 04 Jan 20171 minute 59 seconds
Preliminary analysis of coverage distribution22:41:10 04 Jan 201722:43:16 04 Jan 20172 minutes 6 seconds
Identifying junction candidates22:43:16 04 Jan 201722:54:00 04 Jan 201710 minutes 44 seconds
Re-alignment to junction candidates22:54:00 04 Jan 201722:54:40 04 Jan 201740 seconds
Resolving alignments with junction candidates22:54:40 04 Jan 201722:57:51 04 Jan 20173 minutes 11 seconds
Creating BAM files22:57:51 04 Jan 201722:59:04 04 Jan 20171 minute 13 seconds
Tabulating error counts22:59:04 04 Jan 201723:01:22 04 Jan 20172 minutes 18 seconds
Re-calibrating base error rates23:01:22 04 Jan 201723:01:22 04 Jan 20170 seconds
Examining read alignment evidence23:01:22 04 Jan 201723:18:03 04 Jan 201716 minutes 41 seconds
Polymorphism statistics23:18:03 04 Jan 201723:18:05 04 Jan 20172 seconds
Output23:18:06 04 Jan 201723:19:09 04 Jan 20171 minute 3 seconds
Total 44 minutes 1 second