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Detailed information for vg0130331339:

Variant ID: vg0130331339 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 30331339
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATGCCGGTGGACCCAAAAGGAAAAGGGCCGGGAAAAAAAAACGGAAAGAACAGATTTGTACGTACATACCCGGGGAGCCAAAAACAAGCACCACTATTC[G/A]
ATGGGAAAAAAAAACGTGCATAGGCACCAACGATCGAGTAAAACAAACGATCAATAATTTCAATAAATCAGTGAACCCACTATTTTTACCCCAACAAAAC

Reverse complement sequence

GTTTTGTTGGGGTAAAAATAGTGGGTTCACTGATTTATTGAAATTATTGATCGTTTGTTTTACTCGATCGTTGGTGCCTATGCACGTTTTTTTTTCCCAT[C/T]
GAATAGTGGTGCTTGTTTTTGGCTCCCCGGGTATGTACGTACAAATCTGTTCTTTCCGTTTTTTTTTCCCGGCCCTTTTCCTTTTGGGTCCACCGGCATA

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	97.60%	2.00%	0.42%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	92.70%	6.00%	1.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	98.40%	0.00%	1.56%	0.00%	NA
Tropical Japonica	504	81.20%	18.10%	0.79%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0130331339	G -> A	LOC_Os01g52730-LOC_Os01g52740	intergenic_region ; MODIFIER	silent_mutation	Average:50.669; most accessible tissue: Minghui63 flower, score: 77.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0130331339	5.27E-07	2.91E-06	mr1676	Jap_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