breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-KHP-SSW-3-164-2-1_S17_L001_R2_0011,437,863411,750,042100.0%286.4 bases301 bases93.5%
errorsSSW-KHP-SSW-3-164-2-1_S12_L001_R1_001113,23534,033,947100.0%300.6 bases301 bases81.0%
errorsSSW-KHP-SSW-3-164-2-1_S12_L001_R2_001113,09833,964,22299.9%300.3 bases301 bases78.6%
errorsSSW-KHP-SSW-3-164-2-1_S17_L001_R1_0011,437,923409,282,179100.0%284.6 bases301 bases97.8%
total3,102,119889,030,390100.0%286.6 bases301 bases94.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652178.52.6100.0%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≤ 10000013873
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 ≤ 500041
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.77014

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 input14:23:45 21 Mar 201614:25:15 21 Mar 20161 minute 30 seconds
Read alignment to reference genome14:25:15 21 Mar 201614:30:51 21 Mar 20165 minutes 36 seconds
Preprocessing alignments for candidate junction identification14:30:51 21 Mar 201614:32:29 21 Mar 20161 minute 38 seconds
Preliminary analysis of coverage distribution14:32:29 21 Mar 201614:36:58 21 Mar 20164 minutes 29 seconds
Identifying junction candidates14:36:58 21 Mar 201614:37:00 21 Mar 20162 seconds
Re-alignment to junction candidates14:37:00 21 Mar 201614:37:43 21 Mar 201643 seconds
Resolving alignments with junction candidates14:37:43 21 Mar 201614:42:03 21 Mar 20164 minutes 20 seconds
Creating BAM files14:42:03 21 Mar 201614:44:43 21 Mar 20162 minutes 40 seconds
Tabulating error counts14:44:43 21 Mar 201614:49:17 21 Mar 20164 minutes 34 seconds
Re-calibrating base error rates14:49:17 21 Mar 201614:49:19 21 Mar 20162 seconds
Examining read alignment evidence14:49:19 21 Mar 201615:21:59 21 Mar 201632 minutes 40 seconds
Polymorphism statistics15:21:59 21 Mar 201615:21:59 21 Mar 20160 seconds
Output15:21:59 21 Mar 201615:22:46 21 Mar 201647 seconds
Total 59 minutes 1 second