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Detailed information for vg0100100017:

Variant ID: vg0100100017 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 100017
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, T: 0.38, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TGTCGCTTCAATCCACTTAGTGAATTTATCAATCGCCACGAATAGGAACTTGTAGCCGCCCTGTCCTCGTGGGAATGGGCCGAGTATATCTAGCCCCCAG[T/C]
ACGAGAACGGCCAAGTGAGAGGGATGGTCTGGAGTGCTTGCGCTGGTAGCCTTGTGTGTTTACTGTGGAATTGACAGCTTCACACCGCTAAACCATGTCG

Reverse complement sequence

CGACATGGTTTAGCGGTGTGAAGCTGTCAATTCCACAGTAAACACACAAGGCTACCAGCGCAAGCACTCCAGACCATCCCTCTCACTTGGCCGTTCTCGT[A/G]
CTGGGGGCTAGATATACTCGGCCCATTCCCACGAGGACAGGGCGGCTACAAGTTCCTATTCGTGGCGATTGATAAATTCACTAAGTGGATTGAAGCGACA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.20% 24.80% 0.00% 0.00% NA
All Indica  2759 68.90% 31.10% 0.00% 0.00% NA
All Japonica  1512 97.60% 2.40% 0.00% 0.00% NA
Aus  269 9.30% 90.70% 0.00% 0.00% NA
Indica I  595 28.40% 71.60% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 85.90% 14.10% 0.00% 0.00% NA
Indica Intermediate  786 63.40% 36.60% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 93.80% 6.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0100100017 T -> C LOC_Os01g01200.1 downstream_gene_variant ; 1459.0bp to feature; MODIFIER silent_mutation Average:42.242; most accessible tissue: Minghui63 root, score: 63.193 N N N N
vg0100100017 T -> C LOC_Os01g01210.1 intron_variant ; MODIFIER silent_mutation Average:42.242; most accessible tissue: Minghui63 root, score: 63.193 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0100100017 NA 2.22E-10 mr1662 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
vg0100100017 3.18E-06 NA mr1718 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
vg0100100017 NA 3.21E-06 mr1265_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
vg0100100017 NA 8.86E-07 mr1528_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