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Detailed information for vg1001523112:

Variant ID: vg1001523112 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1523112
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.28, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:

AACACATGGACGTCACTGTGTCATACCACATCAGTGCATGGAGCGGGTTGCACTATACTATAGAAACGAATTTTCTAGACGAGAGCCCCTCGTTGCAGGT[A/G]
AGCCATAACTGCTCGTATCTACGAAAGTTGCTCCCCCCGGAGGGCAGTTCAGAGGCCGCATGCAAAGATCGGTTTTGGCCGTCTACAAAAACAGTTACTC

Reverse complement sequence

GAGTAACTGTTTTTGTAGACGGCCAAAACCGATCTTTGCATGCGGCCTCTGAACTGCCCTCCGGGGGGAGCAACTTTCGTAGATACGAGCAGTTATGGCT[T/C]
ACCTGCAACGAGGGGCTCTCGTCTAGAAAATTCGTTTCTATAGTATAGTGCAACCCGCTCCATGCACTGATGTGGTATGACACAGTGACGTCCATGTGTT

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	35.30%	34.50%	0.78%	29.41%	NA
All Indica	2759	55.90%	3.00%	0.94%	40.20%	NA
All Japonica	1512	1.20%	93.50%	0.00%	5.29%	NA
Aus	269	31.20%	1.10%	4.09%	63.57%	NA
Indica I	595	56.80%	2.40%	1.18%	39.66%	NA
Indica II	465	65.80%	3.70%	1.29%	29.25%	NA
Indica III	913	50.70%	1.20%	0.33%	47.75%	NA
Indica Intermediate	786	55.20%	5.20%	1.27%	38.30%	NA
Temperate Japonica	767	0.90%	98.00%	0.00%	1.04%	NA
Tropical Japonica	504	1.80%	85.10%	0.00%	13.10%	NA
Japonica Intermediate	241	0.80%	96.70%	0.00%	2.49%	NA
VI/Aromatic	96	0.00%	88.50%	0.00%	11.46%	NA
Intermediate	90	26.70%	52.20%	0.00%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001523112	A -> G	LOC_Os10g03520.1	upstream_gene_variant ; 547.0bp to feature; MODIFIER	silent_mutation	Average:35.999; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg1001523112	A -> G	LOC_Os10g03530.1	downstream_gene_variant ; 2400.0bp to feature; MODIFIER	silent_mutation	Average:35.999; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg1001523112	A -> G	LOC_Os10g03510-LOC_Os10g03520	intergenic_region ; MODIFIER	silent_mutation	Average:35.999; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg1001523112	A -> DEL	N	N	silent_mutation	Average:35.999; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001523112	4.63E-06	6.40E-06	mr1959_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