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Detailed information for vg1010010984:

Variant ID: vg1010010984 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10010984
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

GATAAAAAAGAGAAAGGAACAGGGAGTCTACAAATTGATACGTGCGTGGTACACGGATATGGGGACGTGGGAGGTTTTGGTATTCTAAGATAGATCTAAT[G/A]
AAGTCCACCGATTTAAATGAATGTGGATGGTTAGATTTCTCTATTTTATTAGGGTGCCATGTGACGGTTTGGAAGTGTTTGTAGGAAATTTAATGGATTT

Reverse complement sequence

AAATCCATTAAATTTCCTACAAACACTTCCAAACCGTCACATGGCACCCTAATAAAATAGAGAAATCTAACCATCCACATTCATTTAAATCGGTGGACTT[C/T]
ATTAGATCTATCTTAGAATACCAAAACCTCCCACGTCCCCATATCCGTGTACCACGCACGTATCAATTTGTAGACTCCCTGTTCCTTTCTCTTTTTTATC

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	81.90%	15.80%	2.14%	0.21%	NA
All Indica	2759	69.70%	26.50%	3.52%	0.36%	NA
All Japonica	1512	99.40%	0.50%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	31.60%	58.20%	9.08%	1.18%	NA
Indica II	465	85.80%	11.20%	3.01%	0.00%	NA
Indica III	913	83.70%	15.30%	0.99%	0.00%	NA
Indica Intermediate	786	72.60%	24.40%	2.54%	0.38%	NA
Temperate Japonica	767	99.30%	0.50%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	2.22%	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
vg1010010984	G -> A	LOC_Os10g19950.1	upstream_gene_variant ; 4392.0bp to feature; MODIFIER	silent_mutation	Average:33.725; most accessible tissue: Callus, score: 56.93	N	N	N	N
vg1010010984	G -> A	LOC_Os10g19960.1	downstream_gene_variant ; 985.0bp to feature; MODIFIER	silent_mutation	Average:33.725; most accessible tissue: Callus, score: 56.93	N	N	N	N
vg1010010984	G -> A	LOC_Os10g19950-LOC_Os10g19960	intergenic_region ; MODIFIER	silent_mutation	Average:33.725; most accessible tissue: Callus, score: 56.93	N	N	N	N
vg1010010984	G -> DEL	N	N	silent_mutation	Average:33.725; most accessible tissue: Callus, score: 56.93	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010010984	4.12E-06	NA	mr1168_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
vg1010010984	8.71E-06	NA	mr1234_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