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Detailed information for vg0812490623:

Variant ID: vg0812490623 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 12490623
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTGACTGCCCTCACCGGTAGCAGCGCTTCTCCTGGTTGTCACCATCTGAAAATCCCTCACAGAACCAGCAAACAGAGAGAGCTGACTATTAAAACTAAC[C/T]
ACCCACGACTACCATAATTCTTGAATTTATTTCTATTATTAAATTGGTTCATTAAGGTTCAAGTTGCTTATGCAAATAAAATAAAGACAGGCTCCGACAC

Reverse complement sequence

GTGTCGGAGCCTGTCTTTATTTTATTTGCATAAGCAACTTGAACCTTAATGAACCAATTTAATAATAGAAATAAATTCAAGAATTATGGTAGTCGTGGGT[G/A]
GTTAGTTTTAATAGTCAGCTCTCTCTGTTTGCTGGTTCTGTGAGGGATTTTCAGATGGTGACAACCAGGAGAAGCGCTGCTACCGGTGAGGGCAGTCACC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.00% 10.90% 0.06% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 72.40% 27.50% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 44.00% 55.80% 0.20% 0.00% NA
Japonica Intermediate  241 51.50% 48.50% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 81.20% 2.08% 0.00% NA
Intermediate  90 78.90% 21.10% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0812490623 C -> T LOC_Os08g20790.1 upstream_gene_variant ; 1912.0bp to feature; MODIFIER silent_mutation Average:50.194; most accessible tissue: Minghui63 flag leaf, score: 74.161 N N N N
vg0812490623 C -> T LOC_Os08g20820.1 downstream_gene_variant ; 4631.0bp to feature; MODIFIER silent_mutation Average:50.194; most accessible tissue: Minghui63 flag leaf, score: 74.161 N N N N
vg0812490623 C -> T LOC_Os08g20800.1 intron_variant ; MODIFIER silent_mutation Average:50.194; most accessible tissue: Minghui63 flag leaf, score: 74.161 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0812490623 NA 1.26E-12 mr1084 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
vg0812490623 NA 1.48E-06 mr1206 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
vg0812490623 NA 7.91E-07 mr1194_2 Jap_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
vg0812490623 NA 2.80E-08 mr1746_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