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Detailed information for vg0414233780:

Variant ID: vg0414233780 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14233780
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCACTCGGTGCAAGGGGGGACCTGTCTCGTCCTGGGGGATCCGGCATCCTTTACCTTGTCGGGGACCGGCGGGCGGCGAAACCTCAGCGGGTTCTCCT[G/A]
TTTTGGGTAGACCTAGATGGATAGTCTTGTCACGACCTCTATTCGAGTACTGTGATAGTACCCGGTGCGTGGTAACGTGTGTTGAGGTTGTGTCTTGTGG

Reverse complement sequence

CCACAAGACACAACCTCAACACACGTTACCACGCACCGGGTACTATCACAGTACTCGAATAGAGGTCGTGACAAGACTATCCATCTAGGTCTACCCAAAA[C/T]
AGGAGAACCCGCTGAGGTTTCGCCGCCCGCCGGTCCCCGACAAGGTAAAGGATGCCGGATCCCCCAGGACGAGACAGGTCCCCCCTTGCACCGAGTGAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.20%	22.20%	20.02%	9.65%	NA
All Indica	2759	44.20%	15.80%	26.60%	13.41%	NA
All Japonica	1512	54.40%	35.50%	8.60%	1.52%	NA
Aus	269	55.40%	7.40%	15.99%	21.19%	NA
Indica I	595	43.40%	11.40%	32.27%	12.94%	NA
Indica II	465	57.80%	5.40%	16.99%	19.78%	NA
Indica III	913	44.00%	24.10%	23.55%	8.32%	NA
Indica Intermediate	786	36.90%	15.60%	31.55%	15.90%	NA
Temperate Japonica	767	91.80%	5.20%	2.61%	0.39%	NA
Tropical Japonica	504	6.70%	73.00%	16.87%	3.37%	NA
Japonica Intermediate	241	34.90%	53.50%	10.37%	1.24%	NA
VI/Aromatic	96	41.70%	35.40%	18.75%	4.17%	NA
Intermediate	90	51.10%	23.30%	23.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414233780	G -> DEL	N	N	silent_mutation	Average:18.324; most accessible tissue: Callus, score: 56.016	N	N	N	N
vg0414233780	G -> A	LOC_Os04g24780.1	upstream_gene_variant ; 923.0bp to feature; MODIFIER	silent_mutation	Average:18.324; most accessible tissue: Callus, score: 56.016	N	N	N	N
vg0414233780	G -> A	LOC_Os04g24770-LOC_Os04g24780	intergenic_region ; MODIFIER	silent_mutation	Average:18.324; most accessible tissue: Callus, score: 56.016	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414233780	NA	1.05E-06	mr1213	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
vg0414233780	NA	6.20E-06	mr1224_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
vg0414233780	NA	3.23E-06	mr1404_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
vg0414233780	2.16E-06	NA	mr1662_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