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Detailed information for vg1003382071:

Variant ID: vg1003382071 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3382071
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTTCATAACTCGCCTATAAACCGCAAAGCGAAAGTTTGAGCCTAATTAATCTGTCATTACCTAATTTCATAACTCGCATAGAACTTTCACCTAATTCC[A/G]
TCATTACCTAATTCCATAACTCGCCTATAAACCGCGAAGCGAAAGTTTGAGCCTAATTAATCTATCGTTAACTAATTTCATAACTTGTCTGGAACTTTCA

Reverse complement sequence

TGAAAGTTCCAGACAAGTTATGAAATTAGTTAACGATAGATTAATTAGGCTCAAACTTTCGCTTCGCGGTTTATAGGCGAGTTATGGAATTAGGTAATGA[T/C]
GGAATTAGGTGAAAGTTCTATGCGAGTTATGAAATTAGGTAATGACAGATTAATTAGGCTCAAACTTTCGCTTTGCGGTTTATAGGCGAGTTATGAAATT

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	41.00%	27.20%	0.36%	31.38%	NA
All Indica	2759	57.20%	4.80%	0.22%	37.84%	NA
All Japonica	1512	2.00%	72.20%	0.40%	25.46%	NA
Aus	269	92.90%	3.70%	0.37%	2.97%	NA
Indica I	595	54.10%	2.20%	0.34%	43.36%	NA
Indica II	465	75.30%	1.10%	0.00%	23.66%	NA
Indica III	913	41.30%	9.60%	0.33%	48.74%	NA
Indica Intermediate	786	67.20%	3.30%	0.13%	29.39%	NA
Temperate Japonica	767	0.80%	61.50%	0.52%	37.16%	NA
Tropical Japonica	504	3.80%	87.90%	0.00%	8.33%	NA
Japonica Intermediate	241	2.10%	73.00%	0.83%	24.07%	NA
VI/Aromatic	96	42.70%	24.00%	2.08%	31.25%	NA
Intermediate	90	45.60%	34.40%	2.22%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003382071	A -> G	LOC_Os10g06560.1	upstream_gene_variant ; 3562.0bp to feature; MODIFIER	silent_mutation	Average:20.288; most accessible tissue: Zhenshan97 flower, score: 46.765	N	N	N	N
vg1003382071	A -> G	LOC_Os10g06560-LOC_Os10g06580	intergenic_region ; MODIFIER	silent_mutation	Average:20.288; most accessible tissue: Zhenshan97 flower, score: 46.765	N	N	N	N
vg1003382071	A -> DEL	N	N	silent_mutation	Average:20.288; most accessible tissue: Zhenshan97 flower, score: 46.765	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003382071	8.53E-07	1.08E-06	mr1768	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
vg1003382071	NA	6.50E-06	mr1547_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