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Detailed information for vg0405891709:

Variant ID: vg0405891709 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5891709
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.01, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


GCAATGGCGAATGCTATCAGTAAGGTAATGCCGGGTGCTTACCATAGATTGTGTATTTGGCATATAGAGGAGAATATGAGTCGTCACCTTCGTAAGCCAA[C/A]
ACTTGATGAGCTAAGAAAATTAATTTATGCGAGTATGGATGAGGAGGAGTTCGAGAGACGCTTGGGCTGATTTTAAGGAGAATGGAGGCATGGGAAATGG

Reverse complement sequence

CCATTTCCCATGCCTCCATTCTCCTTAAAATCAGCCCAAGCGTCTCTCGAACTCCTCCTCATCCATACTCGCATAAATTAATTTTCTTAGCTCATCAAGT[G/T]
TTGGCTTACGAAGGTGACGACTCATATTCTCCTCTATATGCCAAATACACAATCTATGGTAAGCACCCGGCATTACCTTACTGATAGCATTCGCCATTGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 21.30% 5.70% 0.99% 72.01% NA
All Indica  2759 2.40% 6.50% 1.16% 89.96% NA
All Japonica  1512 60.00% 4.40% 0.46% 35.12% NA
Aus  269 3.30% 6.30% 1.86% 88.48% NA
Indica I  595 2.70% 0.50% 1.34% 95.46% NA
Indica II  465 3.90% 10.10% 1.08% 84.95% NA
Indica III  913 0.90% 10.00% 1.31% 87.84% NA
Indica Intermediate  786 3.20% 4.70% 0.89% 91.22% NA
Temperate Japonica  767 66.60% 3.30% 0.65% 29.47% NA
Tropical Japonica  504 43.50% 5.20% 0.40% 50.99% NA
Japonica Intermediate  241 73.40% 6.60% 0.00% 19.92% NA
VI/Aromatic  96 2.10% 4.20% 0.00% 93.75% NA
Intermediate  90 23.30% 4.40% 3.33% 68.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0405891709 C -> DEL N N silent_mutation Average:11.588; most accessible tissue: Callus, score: 53.106 N N N N
vg0405891709 C -> A LOC_Os04g10850.1 upstream_gene_variant ; 1951.0bp to feature; MODIFIER silent_mutation Average:11.588; most accessible tissue: Callus, score: 53.106 N N N N
vg0405891709 C -> A LOC_Os04g10870.1 downstream_gene_variant ; 2712.0bp to feature; MODIFIER silent_mutation Average:11.588; most accessible tissue: Callus, score: 53.106 N N N N
vg0405891709 C -> A LOC_Os04g10860.1 intron_variant ; MODIFIER silent_mutation Average:11.588; most accessible tissue: Callus, score: 53.106 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405891709 NA 5.82E-15 mr1059 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 1.36E-15 mr1143 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 3.36E-16 mr1167 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 5.90E-07 1.07E-09 mr1227 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 4.29E-06 mr1227 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 2.45E-15 mr1535 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 2.09E-15 mr1675 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 2.06E-08 mr1677 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 1.23E-07 mr1680 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 4.00E-22 mr1698 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 7.68E-15 mr1726 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 4.04E-10 mr1866 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 6.96E-14 mr1940 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 1.25E-15 mr1969 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 1.45E-18 mr1995 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 2.26E-14 mr1035_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 6.68E-06 mr1080_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 3.05E-06 NA mr1100_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 9.21E-08 mr1100_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 8.11E-06 NA mr1203_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 4.21E-06 mr1203_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 7.41E-06 mr1613_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 3.68E-07 mr1748_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 1.87E-06 2.22E-06 mr1913_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405891709 NA 9.20E-06 mr1962_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251