breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSNFR_3_67_0_S2330_L001_R1_001.good.fq947,117133,505,066100.0%141.0 bases141 bases98.9%
errorsSNFR_3_67_0_S2330_L001_R2_001.good.fq947,117133,505,066100.0%141.0 bases141 bases94.3%
total1,894,234267,010,132100.0%141.0 bases141 bases96.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91583.94.094.3%Staphylococcus species strain strain.
coveragedistributionCP00073127,041382.66.44.1%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,1251379.615.01.6%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
total2,903,081100.0%

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≤ 1000004748
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500097
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.010

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.80101
CP0007310.42481
NC_0124170.14399

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 cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
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 ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input20:18:25 25 May 201920:18:53 25 May 201928 seconds
Read alignment to reference genome20:18:53 25 May 201920:23:36 25 May 20194 minutes 43 seconds
Preprocessing alignments for candidate junction identification20:23:36 25 May 201920:24:04 25 May 201928 seconds
Preliminary analysis of coverage distribution20:24:04 25 May 201920:25:11 25 May 20191 minute 7 seconds
Identifying junction candidates20:25:11 25 May 201920:25:12 25 May 20191 second
Re-alignment to junction candidates20:25:12 25 May 201920:26:17 25 May 20191 minute 5 seconds
Resolving best read alignments20:26:17 25 May 201920:26:59 25 May 201942 seconds
Creating BAM files20:26:59 25 May 201920:28:20 25 May 20191 minute 21 seconds
Tabulating error counts20:28:20 25 May 201920:28:39 25 May 201919 seconds
Re-calibrating base error rates20:28:39 25 May 201920:28:41 25 May 20192 seconds
Examining read alignment evidence20:28:41 25 May 201920:53:32 25 May 201924 minutes 51 seconds
Polymorphism statistics20:53:32 25 May 201920:53:32 25 May 20190 seconds
Output20:53:32 25 May 201920:53:41 25 May 20199 seconds
Total 35 minutes 16 seconds