breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR22894666_R1.good.fq2,574,056332,564,200100.0%129.2 bases135 bases99.6%
errorsSRR22894666_R2.good.fq2,574,056332,569,475100.0%129.2 bases135 bases98.7%
total5,148,112665,133,675100.0%129.2 bases135 bases99.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAnnotation_U21_Trimmed_contig_1491,259271.64.220.2%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_2375,970446.912.025.2%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_3367,983345.36.319.2%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_4286,779316.94.913.7%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_5139,689441.26.39.3%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_662,195210.36.81.9%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_760,419479.16.04.4%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_848,531272.93.92.0%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_910,6611668.317.02.7%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_103,2971881.121.30.9%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_111,7111853.318.20.4%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_121,004280.52.90.0%Pediococcus pentosaceus P. pentosaceus_U21
coveragedistributionAnnotation_U21_Trimmed_contig_13479321.68.00.0%Pediococcus pentosaceus P. pentosaceus_U21
total1,849,977100.0%

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≤ 1000004799
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 ≤ 500088
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.013

Junction Skew Score Calculation

reference sequencepr(no read start)
Annotation_U21_Trimmed_contig_10.68953
Annotation_U21_Trimmed_contig_20.61870
Annotation_U21_Trimmed_contig_30.65369
Annotation_U21_Trimmed_contig_40.66527
Annotation_U21_Trimmed_contig_50.61781
Annotation_U21_Trimmed_contig_60.72831
Annotation_U21_Trimmed_contig_70.60681
Annotation_U21_Trimmed_contig_80.68764
Annotation_U21_Trimmed_contig_90.43217
Annotation_U21_Trimmed_contig_100.41705
Annotation_U21_Trimmed_contig_110.42577
Annotation_U21_Trimmed_contig_120.70539
Annotation_U21_Trimmed_contig_130.74018

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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 cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
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 ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input14:04:22 19 Apr 202314:06:08 19 Apr 20231 minute 46 seconds
Read alignment to reference genome14:06:08 19 Apr 202314:21:06 19 Apr 202314 minutes 58 seconds
Preprocessing alignments for candidate junction identification14:21:06 19 Apr 202314:22:30 19 Apr 20231 minute 24 seconds
Preliminary analysis of coverage distribution14:22:30 19 Apr 202314:24:57 19 Apr 20232 minutes 27 seconds
Identifying junction candidates14:24:57 19 Apr 202314:24:59 19 Apr 20232 seconds
Re-alignment to junction candidates14:24:59 19 Apr 202314:27:34 19 Apr 20232 minutes 35 seconds
Resolving best read alignments14:27:34 19 Apr 202314:29:01 19 Apr 20231 minute 27 seconds
Creating BAM files14:29:01 19 Apr 202314:30:58 19 Apr 20231 minute 57 seconds
Tabulating error counts14:30:58 19 Apr 202314:31:52 19 Apr 202354 seconds
Re-calibrating base error rates14:31:52 19 Apr 202314:31:58 19 Apr 20236 seconds
Examining read alignment evidence14:31:58 19 Apr 202314:43:59 19 Apr 202312 minutes 1 second
Polymorphism statistics14:43:59 19 Apr 202314:44:00 19 Apr 20231 second
Output14:44:00 19 Apr 202314:44:15 19 Apr 202315 seconds
Total 39 minutes 53 seconds