Search for Variation information by Variation ID:

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

Detailed information for vg0713016602:

Variant ID: vg0713016602 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13016602
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.04, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:

ACTTCTAAGGTCACTCGGTCACGGTGGTCACATCGTTTCCACTCGGGGATATACTTCATAATCGCGAAGCAAATGGATGAATCGCAAAGTGGGCCTTAGA[A/G]
TTGATGTCTTTAGATATATCCTTCAAGCCGCGAACTTCGATCAAGTCCCAAGCTTTAGCCGAATTTGTCGCCGAGTGGACTGAGTGCCAAGAAGACATGC

Reverse complement sequence

GCATGTCTTCTTGGCACTCAGTCCACTCGGCGACAAATTCGGCTAAAGCTTGGGACTTGATCGAAGTTCGCGGCTTGAAGGATATATCTAAAGACATCAA[T/C]
TCTAAGGCCCACTTTGCGATTCATCCATTTGCTTCGCGATTATGAAGTATATCCCCGAGTGGAAACGATGTGACCACCGTGACCGAGTGACCTTAGAAGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.80%	19.70%	35.53%	1.95%	NA
All Indica	2759	26.40%	25.80%	47.81%	0.00%	NA
All Japonica	1512	78.80%	6.50%	8.93%	5.82%	NA
Aus	269	21.90%	19.00%	57.62%	1.49%	NA
Indica I	595	44.00%	11.60%	44.37%	0.00%	NA
Indica II	465	21.10%	37.40%	41.51%	0.00%	NA
Indica III	913	15.90%	29.20%	54.87%	0.00%	NA
Indica Intermediate	786	28.40%	25.70%	45.93%	0.00%	NA
Temperate Japonica	767	72.90%	2.60%	13.56%	10.95%	NA
Tropical Japonica	504	86.50%	10.50%	2.98%	0.00%	NA
Japonica Intermediate	241	81.30%	10.40%	6.64%	1.66%	NA
VI/Aromatic	96	2.10%	49.00%	48.96%	0.00%	NA
Intermediate	90	48.90%	25.60%	25.56%	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
vg0713016602	A -> DEL	N	N	silent_mutation	Average:10.467; most accessible tissue: Callus, score: 32.326	N	N	N	N
vg0713016602	A -> G	LOC_Os07g23090.1	upstream_gene_variant ; 4011.0bp to feature; MODIFIER	silent_mutation	Average:10.467; most accessible tissue: Callus, score: 32.326	N	N	N	N
vg0713016602	A -> G	LOC_Os07g23080.1	downstream_gene_variant ; 2379.0bp to feature; MODIFIER	silent_mutation	Average:10.467; most accessible tissue: Callus, score: 32.326	N	N	N	N
vg0713016602	A -> G	LOC_Os07g23070.1	intron_variant ; MODIFIER	silent_mutation	Average:10.467; most accessible tissue: Callus, score: 32.326	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713016602	3.74E-06	NA	mr1233_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