Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0404350815:

Variant ID: vg0404350815 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4350815
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTTCAGGAACAATGTTATTCTTGTTCATTTTTTAGATTGGAACAATTATGTGGATTGTTGACCATGTATACTCCAATAGTTCACACATTCCAATTTTC[C/T]
AAGAAACCAGGCATTAGTGGTGATAATTGTTAAGGTACATGCTAATTAAGTACATTTGGTTAATTGGATCTGTGTGACTGAAAGGAATAATGATTATTTT

Reverse complement sequence

AAAATAATCATTATTCCTTTCAGTCACACAGATCCAATTAACCAAATGTACTTAATTAGCATGTACCTTAACAATTATCACCACTAATGCCTGGTTTCTT[G/A]
GAAAATTGGAATGTGTGAACTATTGGAGTATACATGGTCAACAATCCACATAATTGTTCCAATCTAAAAAATGAACAAGAATAACATTGTTCCTGAAAAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.80%	24.90%	1.59%	27.70%	NA
All Indica	2759	23.80%	38.40%	1.88%	35.85%	NA
All Japonica	1512	90.10%	1.20%	0.79%	7.94%	NA
Aus	269	18.60%	28.60%	2.97%	49.81%	NA
Indica I	595	8.20%	89.60%	0.50%	1.68%	NA
Indica II	465	54.20%	13.30%	0.22%	32.26%	NA
Indica III	913	8.90%	25.70%	3.72%	61.66%	NA
Indica Intermediate	786	35.10%	29.30%	1.78%	33.84%	NA
Temperate Japonica	767	95.30%	0.70%	0.39%	3.65%	NA
Tropical Japonica	504	90.90%	1.00%	1.59%	6.55%	NA
Japonica Intermediate	241	71.80%	3.30%	0.41%	24.48%	NA
VI/Aromatic	96	47.90%	4.20%	2.08%	45.83%	NA
Intermediate	90	55.60%	18.90%	1.11%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404350815	C -> DEL	N	N	silent_mutation	Average:38.43; most accessible tissue: Callus, score: 76.976	N	N	N	N
vg0404350815	C -> T	LOC_Os04g08190.1	upstream_gene_variant ; 2325.0bp to feature; MODIFIER	silent_mutation	Average:38.43; most accessible tissue: Callus, score: 76.976	N	N	N	N
vg0404350815	C -> T	LOC_Os04g08170.1	downstream_gene_variant ; 4602.0bp to feature; MODIFIER	silent_mutation	Average:38.43; most accessible tissue: Callus, score: 76.976	N	N	N	N
vg0404350815	C -> T	LOC_Os04g08180.1	intron_variant ; MODIFIER	silent_mutation	Average:38.43; most accessible tissue: Callus, score: 76.976	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404350815	1.62E-06	1.62E-06	mr1377	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