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Detailed information for vg0139981469:

Variant ID: vg0139981469 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39981469
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

GCTATATATAGTAGTTATTCTAATTCACATCGAATCGGATACGAGCGACATACAACCAGCTCAAAATCTGACTCAAACACGGATGACGTTCCAAAATTTT[G/A]
GCGAAAACATCTTCAATTTTTATATTTTTATTAATTATTAATTCATATGGTAGCTTTATACTAGCTCTATAGTTTTGTGATATATCGACTTAGATATGTG

Reverse complement sequence

CACATATCTAAGTCGATATATCACAAAACTATAGAGCTAGTATAAAGCTACCATATGAATTAATAATTAATAAAAATATAAAAATTGAAGATGTTTTCGC[C/T]
AAAATTTTGGAACGTCATCCGTGTTTGAGTCAGATTTTGAGCTGGTTGTATGTCGCTCGTATCCGATTCGATGTGAATTAGAATAACTACTATATATAGC

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	62.00%	38.00%	0.06%	0.00%	NA
All Indica	2759	92.70%	7.20%	0.07%	0.00%	NA
All Japonica	1512	2.20%	97.80%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.20%	1.70%	0.17%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	92.80%	7.20%	0.00%	0.00%	NA
Indica Intermediate	786	85.50%	14.40%	0.13%	0.00%	NA
Temperate Japonica	767	1.60%	98.40%	0.00%	0.00%	NA
Tropical Japonica	504	2.20%	97.80%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.40%	0.41%	0.00%	NA
VI/Aromatic	96	25.00%	75.00%	0.00%	0.00%	NA
Intermediate	90	48.90%	51.10%	0.00%	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
vg0139981469	G -> A	LOC_Os01g68820.1	upstream_gene_variant ; 3754.0bp to feature; MODIFIER	silent_mutation	Average:48.892; most accessible tissue: Minghui63 root, score: 62.438	N	N	N	N
vg0139981469	G -> A	LOC_Os01g68810-LOC_Os01g68820	intergenic_region ; MODIFIER	silent_mutation	Average:48.892; most accessible tissue: Minghui63 root, score: 62.438	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0139981469	NA	8.30E-66	mr1027	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
vg0139981469	NA	1.68E-28	mr1075	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
vg0139981469	NA	4.55E-06	mr1119	Ind_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
vg0139981469	1.29E-06	NA	mr1121	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
vg0139981469	NA	4.02E-06	mr1121	Ind_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
vg0139981469	NA	1.55E-22	mr1155	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
vg0139981469	NA	3.93E-07	mr1162	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
vg0139981469	NA	5.94E-11	mr1281	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
vg0139981469	NA	6.53E-11	mr1630	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
vg0139981469	NA	7.35E-23	mr1888	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
vg0139981469	NA	2.56E-11	mr1902	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
vg0139981469	NA	1.16E-36	mr1155_2	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
vg0139981469	NA	6.10E-11	mr1216_2	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
vg0139981469	NA	1.64E-06	mr1533_2	Ind_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