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_23_171_0_S171_S1997_L006_R1_001.good.fq1,193,957166,791,205100.0%139.7 bases141 bases95.4%
errorsSNFR_23_171_0_S171_S1997_L006_R2_001.good.fq1,193,957166,791,205100.0%139.7 bases141 bases93.9%
errorsSNFR_23_171_0_S171_S1997_L008_R1_001.good.fq506,18770,648,061100.0%139.6 bases141 bases95.4%
errorsSNFR_23_171_0_S171_S1997_L008_R2_001.good.fq506,18770,648,061100.0%139.6 bases141 bases92.4%
total3,400,288474,878,532100.0%139.7 bases141 bases94.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,915151.82.297.8%Staphylococcus species strain strain.
coveragedistributionCP00073127,041NANA0.0%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,1253426.26.42.2%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.

Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing or the -c,--contig-reference option if you want mutations called for these reference sequences.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 10000070625
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 ≤ 5000158
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.016

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.63521
CP0007310.99413
NC_0124170.05567

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 input06:00:39 25 May 201906:01:26 25 May 201947 seconds
Read alignment to reference genome06:01:26 25 May 201906:09:14 25 May 20197 minutes 48 seconds
Preprocessing alignments for candidate junction identification06:09:14 25 May 201906:10:04 25 May 201950 seconds
Preliminary analysis of coverage distribution06:10:04 25 May 201906:11:42 25 May 20191 minute 38 seconds
Identifying junction candidates06:11:42 25 May 201906:12:05 25 May 201923 seconds
Re-alignment to junction candidates06:12:05 25 May 201906:14:05 25 May 20192 minutes 0 seconds
Resolving best read alignments06:14:05 25 May 201906:15:17 25 May 20191 minute 12 seconds
Creating BAM files06:15:17 25 May 201906:16:42 25 May 20191 minute 25 seconds
Tabulating error counts06:16:42 25 May 201906:17:19 25 May 201937 seconds
Re-calibrating base error rates06:17:19 25 May 201906:17:21 25 May 20192 seconds
Examining read alignment evidence06:17:21 25 May 201906:51:20 25 May 201933 minutes 59 seconds
Polymorphism statistics06:51:20 25 May 201906:51:21 25 May 20191 second
Output06:51:21 25 May 201906:51:37 25 May 201916 seconds
Total 50 minutes 58 seconds