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Detailed information for vg0115329766:

Variant ID: vg0115329766 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15329766
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCCAAAATTTATGATTTAGCCTTACACCAGCACGATACGTGTTACTCCATCCTAAGCCATACACGTTATATGACCTAGAACCGTTAAGTTTAAGTGGT[G/A]
GGCCCACGCCTTAAACTTAACGCCATGGTGGCGAACACAACGGGACCCCACCCACGTGGCACAATACCATTGTATTAGATAGAGTTAGTCACCTAAACTA

Reverse complement sequence

TAGTTTAGGTGACTAACTCTATCTAATACAATGGTATTGTGCCACGTGGGTGGGGTCCCGTTGTGTTCGCCACCATGGCGTTAAGTTTAAGGCGTGGGCC[C/T]
ACCACTTAAACTTAACGGTTCTAGGTCATATAACGTGTATGGCTTAGGATGGAGTAACACGTATCGTGCTGGTGTAAGGCTAAATCATAAATTTTGGAAA

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	52.30%	20.80%	0.47%	26.47%	NA
All Indica	2759	32.30%	30.50%	0.69%	36.53%	NA
All Japonica	1512	87.80%	0.10%	0.07%	12.04%	NA
Aus	269	41.60%	42.00%	0.00%	16.36%	NA
Indica I	595	45.40%	5.70%	0.67%	48.24%	NA
Indica II	465	20.60%	46.50%	1.51%	31.40%	NA
Indica III	913	31.80%	40.30%	0.44%	27.49%	NA
Indica Intermediate	786	29.80%	28.50%	0.51%	41.22%	NA
Temperate Japonica	767	95.20%	0.00%	0.00%	4.82%	NA
Tropical Japonica	504	93.80%	0.00%	0.20%	5.95%	NA
Japonica Intermediate	241	51.90%	0.40%	0.00%	47.72%	NA
VI/Aromatic	96	92.70%	6.20%	0.00%	1.04%	NA
Intermediate	90	58.90%	21.10%	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
vg0115329766	G -> A	LOC_Os01g27449.1	intron_variant ; MODIFIER	silent_mutation	Average:43.22; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg0115329766	G -> DEL	N	N	silent_mutation	Average:43.22; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115329766	NA	3.30E-08	mr1403_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
vg0115329766	NA	2.95E-06	mr1519_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