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Detailed information for vg1019221664:

Variant ID: vg1019221664 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 19221664
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCTAGGATTGTTTTTTTCCCCTCAGCTGCTGGAGCTAAAATATTTTATTGTAACAGAAGATTTTCCAGTGCTTCTGTGCTTGTGCTTGAACTAATTCA[G/A]
CTTTATACTGATCATCAGGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAGGTAAGAATCAACAATT

Reverse complement sequence

AATTGTTGATTCTTACCTCCTCATTAAATATGCCCCCAACTCCAGAAAGTCCTAAAAGCACATGAGGCTTCACTTTCCTGACCTGATGATCAGTATAAAG[C/T]
TGAATTAGTTCAAGCACAAGCACAGAAGCACTGGAAAATCTTCTGTTACAATAAAATATTTTAGCTCCAGCAGCTGAGGGGAAAAAAACAATCCTAGAAT

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	91.20%	8.70%	0.06%	0.00%	NA
All Indica	2759	85.70%	14.20%	0.11%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	94.80%	5.20%	0.00%	0.00%	NA
Indica I	595	82.50%	17.50%	0.00%	0.00%	NA
Indica II	465	84.50%	15.30%	0.22%	0.00%	NA
Indica III	913	84.30%	15.40%	0.22%	0.00%	NA
Indica Intermediate	786	90.30%	9.70%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg1019221664	G -> A	LOC_Os10g35960.1	intron_variant ; MODIFIER	silent_mutation	Average:53.88; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N
vg1019221664	G -> A	LOC_Os10g35960.2	intron_variant ; MODIFIER	silent_mutation	Average:53.88; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1019221664	4.41E-06	3.36E-06	mr1817	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
vg1019221664	NA	9.77E-07	mr1925	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