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Detailed information for vg0330416961:

Variant ID: vg0330416961 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 30416961
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTAAATACTGGGGCTGTACATCAGTTATTGAACCCTTTATTTCCAATGGAAATACTTGCCCACCGTTAATTAGCTACTCCCTCCGGGCTGATAATACTT[G/A]
TCGTTTTGAATAAGGGTGAGGTCAAATTTTAGAATCTTTGATTATGAATCATTTTTAAAATATTTGTCTTTTAAATATGGTGACCATATGTATAGATTAG

Reverse complement sequence

CTAATCTATACATATGGTCACCATATTTAAAAGACAAATATTTTAAAAATGATTCATAATCAAAGATTCTAAAATTTGACCTCACCCTTATTCAAAACGA[C/T]
AAGTATTATCAGCCCGGAGGGAGTAGCTAATTAACGGTGGGCAAGTATTTCCATTGGAAATAAAGGGTTCAATAACTGATGTACAGCCCCAGTATTTAAG

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	98.80%	1.00%	0.21%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	96.20%	3.20%	0.60%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	93.70%	5.20%	1.04%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	2.90%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg0330416961	G -> A	LOC_Os03g53030-LOC_Os03g53050	intergenic_region ; MODIFIER	silent_mutation	Average:52.448; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0330416961	7.52E-06	NA	mr1114	Jap_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
vg0330416961	2.14E-06	8.64E-06	mr1496	Jap_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
vg0330416961	1.73E-06	2.78E-06	mr1917	Jap_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
vg0330416961	1.17E-06	9.99E-07	mr1936	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