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Detailed information for vg1014524942:

Variant ID: vg1014524942 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14524942
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, A: 0.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTCGTAACTCGACCACTTGAAGTAAAGGTAGTGGGAGAATCGCTACACCACTGGTCGAGGACCAGGTAGTAGTCGTAACTCGACCACTGGAAGCAAAT[G/A]
TACGAGAGATCACTACGATCAACTGGTTGAGAACCAGTGAGTAGGTGTCTCTCGATCATTTGGAGTCGTGGTACGAGGACCGCTACGCTGCCGGTCGAAG

Reverse complement sequence

CTTCGACCGGCAGCGTAGCGGTCCTCGTACCACGACTCCAAATGATCGAGAGACACCTACTCACTGGTTCTCAACCAGTTGATCGTAGTGATCTCTCGTA[C/T]
ATTTGCTTCCAGTGGTCGAGTTACGACTACTACCTGGTCCTCGACCAGTGGTGTAGCGATTCTCCCACTACCTTTACTTCAAGTGGTCGAGTTACGACTA

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	61.80%	38.20%	0.08%	0.00%	NA
All Indica	2759	35.90%	64.00%	0.14%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	32.40%	67.60%	0.00%	0.00%	NA
Indica II	465	34.80%	64.90%	0.22%	0.00%	NA
Indica III	913	35.30%	64.60%	0.11%	0.00%	NA
Indica Intermediate	786	39.80%	59.90%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	32.20%	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
vg1014524942	G -> A	LOC_Os10g28009.1	upstream_gene_variant ; 4499.0bp to feature; MODIFIER	silent_mutation	Average:49.691; most accessible tissue: Minghui63 young leaf, score: 74.514	N	N	N	N
vg1014524942	G -> A	LOC_Os10g28009-LOC_Os10g28020	intergenic_region ; MODIFIER	silent_mutation	Average:49.691; most accessible tissue: Minghui63 young leaf, score: 74.514	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014524942	6.33E-06	1.85E-06	mr1988	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
vg1014524942	NA	1.17E-06	mr1990	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
vg1014524942	NA	3.80E-07	mr1925_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