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Detailed information for vg1204021413:

Variant ID: vg1204021413 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4021413
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.51, T: 0.51, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

AATTATCAACTTGAGTTGCTGAGGAGCAACCCTGGTAGCACAGTGGTTGTTAACAAGGAAATTGGATTGGATCCCCCAGTGTTCAAGAGAATATAGATTT[T/G]
CCTAGTTGCATGCAAGAAATGGTTTTCAAGTGGATGCAGGAGGGTAATTGGACTAGATGGTTGCTTTTTCAAGGGAGCAACTAATGTAGAGCTATTGTGT

Reverse complement sequence

ACACAATAGCTCTACATTAGTTGCTCCCTTGAAAAAGCAACCATCTAGTCCAATTACCCTCCTGCATCCACTTGAAAACCATTTCTTGCATGCAACTAGG[A/C]
AAATCTATATTCTCTTGAACACTGGGGGATCCAATCCAATTTCCTTGTTAACAACCACTGTGCTACCAGGGTTGCTCCTCAGCAACTCAAGTTGATAATT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.90%	9.50%	0.34%	65.28%	NA
All Indica	2759	3.30%	4.40%	0.33%	91.92%	NA
All Japonica	1512	63.00%	19.20%	0.26%	17.46%	NA
Aus	269	5.60%	5.20%	1.12%	88.10%	NA
Indica I	595	1.70%	0.30%	0.50%	97.48%	NA
Indica II	465	2.40%	16.10%	0.43%	81.08%	NA
Indica III	913	3.70%	1.00%	0.22%	95.07%	NA
Indica Intermediate	786	4.70%	4.60%	0.25%	90.46%	NA
Temperate Japonica	767	83.70%	11.90%	0.00%	4.43%	NA
Tropical Japonica	504	43.10%	26.40%	0.40%	30.16%	NA
Japonica Intermediate	241	39.00%	27.80%	0.83%	32.37%	NA
VI/Aromatic	96	77.10%	8.30%	0.00%	14.58%	NA
Intermediate	90	46.70%	15.60%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204021413	T -> DEL	N	N	silent_mutation	Average:9.365; most accessible tissue: Callus, score: 45.252	N	N	N	N
vg1204021413	T -> G	LOC_Os12g07910.1	downstream_gene_variant ; 1946.0bp to feature; MODIFIER	silent_mutation	Average:9.365; most accessible tissue: Callus, score: 45.252	N	N	N	N
vg1204021413	T -> G	LOC_Os12g07920.1	downstream_gene_variant ; 5.0bp to feature; MODIFIER	silent_mutation	Average:9.365; most accessible tissue: Callus, score: 45.252	N	N	N	N
vg1204021413	T -> G	LOC_Os12g07930.1	downstream_gene_variant ; 1271.0bp to feature; MODIFIER	silent_mutation	Average:9.365; most accessible tissue: Callus, score: 45.252	N	N	N	N
vg1204021413	T -> G	LOC_Os12g07920-LOC_Os12g07930	intergenic_region ; MODIFIER	silent_mutation	Average:9.365; most accessible tissue: Callus, score: 45.252	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204021413	8.59E-07	2.99E-07	mr1871_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