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Detailed information for vg0105078015:

Variant ID: vg0105078015 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5078015
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTGGCGATAGCAATTGAGGCCTGCCTCGCCATCGTCAATGCCGCTGATGGTCGGTAAGAGGGAAAGAGAGAGGTGAGAGTGTCTGGCAGGCTGGCCCA[C/T]
CATTTAAAAAAAAATGATGATTGAATTGTCACGTATACGTCATGTAGGACAGACAGTTTCGGATTGAGTCAAGGGGTTATTCACCTGGTATAGACAGTTC

Reverse complement sequence

GAACTGTCTATACCAGGTGAATAACCCCTTGACTCAATCCGAAACTGTCTGTCCTACATGACGTATACGTGACAATTCAATCATCATTTTTTTTTAAATG[G/A]
TGGGCCAGCCTGCCAGACACTCTCACCTCTCTCTTTCCCTCTTACCGACCATCAGCGGCATTGACGATGGCGAGGCAGGCCTCAATTGCTATCGCCACCC

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	54.70%	44.90%	0.06%	0.36%	NA
All Indica	2759	29.50%	69.80%	0.11%	0.58%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	58.70%	41.30%	0.00%	0.00%	NA
Indica I	595	72.90%	26.20%	0.34%	0.50%	NA
Indica II	465	24.10%	75.70%	0.00%	0.22%	NA
Indica III	913	3.90%	95.80%	0.00%	0.22%	NA
Indica Intermediate	786	29.40%	69.20%	0.13%	1.27%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	75.00%	25.00%	0.00%	0.00%	NA
Intermediate	90	50.00%	48.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0105078015	C -> T	LOC_Os01g09810.1	upstream_gene_variant ; 3085.0bp to feature; MODIFIER	silent_mutation	Average:52.651; most accessible tissue: Minghui63 root, score: 78.346	N	N	N	N
vg0105078015	C -> T	LOC_Os01g09810-LOC_Os01g09830	intergenic_region ; MODIFIER	silent_mutation	Average:52.651; most accessible tissue: Minghui63 root, score: 78.346	N	N	N	N
vg0105078015	C -> DEL	N	N	silent_mutation	Average:52.651; most accessible tissue: Minghui63 root, score: 78.346	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105078015	3.53E-06	NA	mr1916	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
vg0105078015	1.03E-06	1.03E-06	mr1916	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