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-3-164-4-1_S2_L001_R2_001373,286102,148,222100.0%273.6 bases301 bases95.3%
errorsSSW-KHP-SSW-3-164-4-1_S14_L001_R2_001158,66247,647,61099.9%300.3 bases301 bases68.2%
errorsSSW-KHP-SSW-3-164-4-1_S14_L001_R1_001158,87247,752,060100.0%300.6 bases301 bases70.2%
errorsSSW-KHP-SSW-3-164-4-1_S2_L001_R1_001373,295101,805,168100.0%272.7 bases301 bases97.6%
total1,064,115299,353,060100.0%281.3 bases301 bases88.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65256.31.9100.0%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≤ 1000004698
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 ≤ 50009
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.91550

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 input15:22:46 21 Mar 201615:23:18 21 Mar 201632 seconds
Read alignment to reference genome15:23:18 21 Mar 201615:25:14 21 Mar 20161 minute 56 seconds
Preprocessing alignments for candidate junction identification15:25:14 21 Mar 201615:25:45 21 Mar 201631 seconds
Preliminary analysis of coverage distribution15:25:45 21 Mar 201615:27:03 21 Mar 20161 minute 18 seconds
Identifying junction candidates15:27:03 21 Mar 201615:27:04 21 Mar 20161 second
Re-alignment to junction candidates15:27:04 21 Mar 201615:27:17 21 Mar 201613 seconds
Resolving alignments with junction candidates15:27:17 21 Mar 201615:28:23 21 Mar 20161 minute 6 seconds
Creating BAM files15:28:23 21 Mar 201615:29:06 21 Mar 201643 seconds
Tabulating error counts15:29:06 21 Mar 201615:30:32 21 Mar 20161 minute 26 seconds
Re-calibrating base error rates15:30:32 21 Mar 201615:30:34 21 Mar 20162 seconds
Examining read alignment evidence15:30:34 21 Mar 201615:41:38 21 Mar 201611 minutes 4 seconds
Polymorphism statistics15:41:38 21 Mar 201615:41:38 21 Mar 20160 seconds
Output15:41:38 21 Mar 201615:41:56 21 Mar 201618 seconds
Total 19 minutes 10 seconds