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Detailed information for vg0209430779:

Variant ID: vg0209430779 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9430779
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: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CGCCTTTGTCTTCTCTGTGATGATTCTGTGCATGTTGTTGTGAATGTGTATCTACTCTGTCCTCCTATAGTTCATTTCGTGCAATTTAATTTAAGTGTCC[G/A]
CTAGTTTTACAGTTTTTCTGTTGCTCGGAAGTTCCGGTATTTAGAACACCGGAAGTTCCGGACAGTCTGAGCAGACCAGAAGTTTCGGTGTTCTACACCC

Reverse complement sequence

GGGTGTAGAACACCGAAACTTCTGGTCTGCTCAGACTGTCCGGAACTTCCGGTGTTCTAAATACCGGAACTTCCGAGCAACAGAAAAACTGTAAAACTAG[C/T]
GGACACTTAAATTAAATTGCACGAAATGAACTATAGGAGGACAGAGTAGATACACATTCACAACAACATGCACAGAATCATCACAGAGAAGACAAAGGCG

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	96.50%	2.90%	0.59%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	89.40%	8.80%	1.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	98.60%	0.10%	1.30%	0.00%	NA
Tropical Japonica	504	73.60%	23.20%	3.17%	0.00%	NA
Japonica Intermediate	241	93.40%	6.20%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	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
vg0209430779	G -> A	LOC_Os02g16520.1	upstream_gene_variant ; 2457.0bp to feature; MODIFIER	silent_mutation	Average:68.305; most accessible tissue: Minghui63 flag leaf, score: 79.676	N	N	N	N
vg0209430779	G -> A	LOC_Os02g16520-LOC_Os02g16529	intergenic_region ; MODIFIER	silent_mutation	Average:68.305; most accessible tissue: Minghui63 flag leaf, score: 79.676	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209430779	NA	1.89E-07	mr1136	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
vg0209430779	NA	1.04E-06	mr1188	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
vg0209430779	NA	4.21E-07	mr1583	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
vg0209430779	2.49E-08	6.78E-12	mr1218_2	Jap_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
vg0209430779	4.42E-06	4.42E-06	mr1333_2	Jap_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
vg0209430779	NA	2.35E-06	mr1422_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
vg0209430779	NA	2.39E-06	mr1583_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
vg0209430779	NA	1.19E-06	mr1830_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
vg0209430779	NA	5.90E-09	mr1850_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