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Detailed information for vg0227977382:

Variant ID: vg0227977382 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 27977382
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

GGGGTCTGTCCGCAGCCCAACATGACTGTACTCCTACTCTATAATAAAGAGACCTCTGTTGCTGTGATATTCTGTCTTCCTGTGATACCAGCTCTATTTC[C/T]
TGGGATTGGTATCGGTTAACAGGTTAATTTGGAGCGTCACAGGCTGGTTCCGTTCGGGGCTAGTTCGGGGCGTGACATAAGTGAAAACTGATGGTTGGAT

Reverse complement sequence

ATCCAACCATCAGTTTTCACTTATGTCACGCCCCGAACTAGCCCCGAACGGAACCAGCCTGTGACGCTCCAAATTAACCTGTTAACCGATACCAATCCCA[G/A]
GAAATAGAGCTGGTATCACAGGAAGACAGAATATCACAGCAACAGAGGTCTCTTTATTATAGAGTAGGAGTACAGTCATGTTGGGCTGCGGACAGACCCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.70%	4.90%	5.44%	0.00%	NA
All Indica	2759	82.70%	8.20%	9.13%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	69.70%	8.70%	21.51%	0.00%	NA
Indica II	465	63.40%	26.20%	10.32%	0.00%	NA
Indica III	913	99.20%	0.10%	0.66%	0.00%	NA
Indica Intermediate	786	84.70%	6.40%	8.91%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	4.40%	4.44%	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
vg0227977382	C -> T	LOC_Os02g45910.1	downstream_gene_variant ; 205.0bp to feature; MODIFIER	silent_mutation	Average:33.961; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0227977382	C -> T	LOC_Os02g45900-LOC_Os02g45910	intergenic_region ; MODIFIER	silent_mutation	Average:33.961; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0227977382	NA	3.52E-08	mr1117	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