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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsm-tar-PAL-A28-F88-I0-R1_S15_L001_R1_001.good.fq1,518,794454,962,287100.0%299.6 bases300 bases85.1%
errorsm-tar-PAL-A28-F88-I0-R1_S15_L001_R2_001.good.fq1,324,552378,167,355100.0%285.5 bases286 bases87.8%
total2,843,346833,129,642100.0%293.0 bases300 bases86.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652149.22.3100.0%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≤ 1000005419
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 ≤ 5000440
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.057

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.79250

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 input13:10:27 27 Mar 201913:11:25 27 Mar 201958 seconds
Read alignment to reference genome13:11:25 27 Mar 201913:28:47 27 Mar 201917 minutes 22 seconds
Preprocessing alignments for candidate junction identification13:28:47 27 Mar 201913:29:35 27 Mar 201948 seconds
Preliminary analysis of coverage distribution13:29:35 27 Mar 201913:32:08 27 Mar 20192 minutes 33 seconds
Identifying junction candidates13:32:08 27 Mar 201913:32:14 27 Mar 20196 seconds
Re-alignment to junction candidates13:32:14 27 Mar 201913:36:29 27 Mar 20194 minutes 15 seconds
Resolving best read alignments13:36:29 27 Mar 201913:37:57 27 Mar 20191 minute 28 seconds
Creating BAM files13:37:57 27 Mar 201913:40:09 27 Mar 20192 minutes 12 seconds
Tabulating error counts13:40:09 27 Mar 201913:41:10 27 Mar 20191 minute 1 second
Re-calibrating base error rates13:41:10 27 Mar 201913:41:11 27 Mar 20191 second
Examining read alignment evidence13:41:11 27 Mar 201914:42:46 27 Mar 20191 hour 1 minute 35 seconds
Polymorphism statistics14:42:46 27 Mar 201914:42:47 27 Mar 20191 second
Output14:42:47 27 Mar 201914:43:10 27 Mar 201923 seconds
Total 1 hour 32 minutes 43 seconds