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Detailed information for vg1005148582:

Variant ID: vg1005148582 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5148582
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

ACGTAATTCGTCGAGTTATCATATATCTTACATAATCTCTAACAATATCGCCATCTAACCTACAATCGGCTAACATCTGGTGATAGAGGGCAGCCGATTA[G/A]
GTTAAATATCGACGTTGGTTCAGATTATATAAGATATCTACCACTCTATGAAACTTCCAGCGGCTTGATTGTCTAGATATTGTTCTTCTTTTCATACTTA

Reverse complement sequence

TAAGTATGAAAAGAAGAACAATATCTAGACAATCAAGCCGCTGGAAGTTTCATAGAGTGGTAGATATCTTATATAATCTGAACCAACGTCGATATTTAAC[C/T]
TAATCGGCTGCCCTCTATCACCAGATGTTAGCCGATTGTAGGTTAGATGGCGATATTGTTAGAGATTATGTAAGATATATGATAACTCGACGAATTACGT

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	35.10%	17.80%	35.00%	12.08%	NA
All Indica	2759	19.60%	27.00%	48.31%	5.07%	NA
All Japonica	1512	65.90%	5.00%	7.54%	21.56%	NA
Aus	269	12.60%	3.00%	49.81%	34.57%	NA
Indica I	595	17.80%	20.20%	59.66%	2.35%	NA
Indica II	465	12.50%	29.90%	50.75%	6.88%	NA
Indica III	913	24.00%	30.90%	40.64%	4.49%	NA
Indica Intermediate	786	20.10%	26.00%	47.20%	6.74%	NA
Temperate Japonica	767	79.40%	1.30%	4.95%	14.34%	NA
Tropical Japonica	504	51.80%	9.30%	8.53%	30.36%	NA
Japonica Intermediate	241	52.30%	7.90%	13.69%	26.14%	NA
VI/Aromatic	96	49.00%	3.10%	38.54%	9.38%	NA
Intermediate	90	46.70%	10.00%	40.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005148582	G -> A	LOC_Os10g09529.1	upstream_gene_variant ; 1138.0bp to feature; MODIFIER	silent_mutation	Average:8.176; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1005148582	G -> A	LOC_Os10g09529-LOC_Os10g09550	intergenic_region ; MODIFIER	silent_mutation	Average:8.176; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1005148582	G -> DEL	N	N	silent_mutation	Average:8.176; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005148582	2.59E-06	2.59E-06	mr1205	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
vg1005148582	NA	1.74E-06	mr1511	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
vg1005148582	1.72E-07	4.41E-07	mr1511	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