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Detailed information for vg1214594843:

Variant ID: vg1214594843 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14594843
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.24, T: 0.01, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTCCTCCTCACCCGTTTGATTTCCTTTAAATCCAACGTACTGAGCAAAGTCCAGAATATTGTCGTCTTACACTTCATCTTCTTCCATTTCAACACCTT[G/A]
CTCTCTGTGGTATGTCCAACAATTATAGCTTGGCATGAACCCCGACTCAAACAAGTGGAAATGAATAGTCCTGGATGCAGAATACTCCTTCTGATTCTTA

Reverse complement sequence

TAAGAATCAGAAGGAGTATTCTGCATCCAGGACTATTCATTTCCACTTGTTTGAGTCGGGGTTCATGCCAAGCTATAATTGTTGGACATACCACAGAGAG[C/T]
AAGGTGTTGAAATGGAAGAAGATGAAGTGTAAGACGACAATATTCTGGACTTTGCTCAGTACGTTGGATTTAAAGGAAATCAAACGGGTGAGGAGGAAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.40% 7.00% 9.08% 5.61% NA
All Indica  2759 66.20% 11.60% 14.72% 7.54% NA
All Japonica  1512 95.30% 0.50% 0.79% 3.44% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 31.80% 38.70% 23.70% 5.88% NA
Indica II  465 80.60% 3.90% 7.96% 7.53% NA
Indica III  913 80.00% 0.40% 12.05% 7.56% NA
Indica Intermediate  786 67.70% 8.50% 15.01% 8.78% NA
Temperate Japonica  767 97.70% 0.10% 0.78% 1.43% NA
Tropical Japonica  504 92.10% 0.80% 0.79% 6.35% NA
Japonica Intermediate  241 94.60% 0.80% 0.83% 3.73% NA
VI/Aromatic  96 95.80% 0.00% 2.08% 2.08% NA
Intermediate  90 83.30% 3.30% 10.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214594843 G -> DEL N N silent_mutation Average:17.616; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg1214594843 G -> A LOC_Os12g25320.1 upstream_gene_variant ; 58.0bp to feature; MODIFIER silent_mutation Average:17.616; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg1214594843 G -> A LOC_Os12g25320-LOC_Os12g25330 intergenic_region ; MODIFIER silent_mutation Average:17.616; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214594843 NA 2.85E-06 mr1308 Ind_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
vg1214594843 NA 2.00E-07 mr1164_2 Ind_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
vg1214594843 NA 8.25E-08 mr1170_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
vg1214594843 NA 1.34E-08 mr1170_2 Ind_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
vg1214594843 8.61E-06 NA mr1308_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
vg1214594843 2.50E-06 1.35E-08 mr1308_2 Ind_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
vg1214594843 2.92E-06 NA mr1361_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
vg1214594843 1.20E-06 8.57E-10 mr1361_2 Ind_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
vg1214594843 NA 8.35E-06 mr1629_2 Ind_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
vg1214594843 NA 6.21E-06 mr1637_2 Ind_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
vg1214594843 NA 2.60E-07 mr1745_2 Ind_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