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Detailed information for vg1005034202:

Variant ID: vg1005034202 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5034202
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

AACTTCCATTCCATGATTGCTCGCAAAACTTTTAGACAAAAAGGAATGTGTAGCACCGAAATCAAAAAGCACAGTTGCGGGTATAGAGTTAACAGGAAAC[G/A]
TACCCAAAACCACATCAGGTGCATTCTAGGCTTCTGCAGCTGCAACGTGATTAACACGAGCCTTCGGTGCTGGAGCATTGGAGTTGTTCTGGACAGGAGC

Reverse complement sequence

GCTCCTGTCCAGAACAACTCCAATGCTCCAGCACCGAAGGCTCGTGTTAATCACGTTGCAGCTGCAGAAGCCTAGAATGCACCTGATGTGGTTTTGGGTA[C/T]
GTTTCCTGTTAACTCTATACCCGCAACTGTGCTTTTTGATTTCGGTGCTACACATTCCTTTTTGTCTAAAAGTTTTGCGAGCAATCATGGAATGGAAGTT

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	45.00%	38.10%	10.03%	6.83%	NA
All Indica	2759	28.50%	55.10%	11.63%	4.78%	NA
All Japonica	1512	71.90%	9.50%	6.22%	12.37%	NA
Aus	269	38.70%	43.90%	16.73%	0.74%	NA
Indica I	595	42.90%	49.70%	6.89%	0.50%	NA
Indica II	465	24.30%	52.70%	11.83%	11.18%	NA
Indica III	913	22.10%	57.10%	14.46%	6.35%	NA
Indica Intermediate	786	27.50%	58.30%	11.83%	2.42%	NA
Temperate Japonica	767	81.60%	3.70%	2.22%	12.52%	NA
Tropical Japonica	504	62.30%	16.70%	10.52%	10.52%	NA
Japonica Intermediate	241	61.00%	13.30%	9.96%	15.77%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	63.30%	21.10%	13.33%	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
vg1005034202	G -> A	LOC_Os10g09300.1	upstream_gene_variant ; 4445.0bp to feature; MODIFIER	silent_mutation	Average:26.857; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N
vg1005034202	G -> A	LOC_Os10g09310.1	intron_variant ; MODIFIER	silent_mutation	Average:26.857; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N
vg1005034202	G -> DEL	N	N	silent_mutation	Average:26.857; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005034202	5.30E-06	NA	mr1788	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
vg1005034202	1.13E-06	2.96E-06	mr1788	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