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Detailed information for vg0522701149:

Variant ID: vg0522701149 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 22701149
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTTGTAGGCGTGTGCATTCTCTGAATTTTTTAGACCCTTCTTCGTGTCAACATGTTGGAGTGTGTGAAGGTGTCATTCATGTAGTACAGTACAAAATG[G/C]
CCTGGCTGACTGTCTCGTCGGATTCTGAATTTCAGGTCAGCAACCATCGATTCAGAATTCAGAGAGAGAGAGAGAGAGAGAGAGTGAGAGAAAGACAGCA

Reverse complement sequence

TGCTGTCTTTCTCTCACTCTCTCTCTCTCTCTCTCTCTCTGAATTCTGAATCGATGGTTGCTGACCTGAAATTCAGAATCCGACGAGACAGTCAGCCAGG[C/G]
CATTTTGTACTGTACTACATGAATGACACCTTCACACACTCCAACATGTTGACACGAAGAAGGGTCTAAAAAATTCAGAGAATGCACACGCCTACAAGCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.40%	5.40%	1.21%	0.00%	NA
All Indica	2759	88.90%	9.10%	2.03%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	96.00%	1.80%	2.18%	0.00%	NA
Indica II	465	92.50%	6.00%	1.51%	0.00%	NA
Indica III	913	84.30%	14.80%	0.88%	0.00%	NA
Indica Intermediate	786	86.60%	9.80%	3.56%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	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	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
vg0522701149	G -> C	LOC_Os05g38690.1	upstream_gene_variant ; 1495.0bp to feature; MODIFIER	silent_mutation	Average:57.252; most accessible tissue: Callus, score: 91.255	N	N	N	N
vg0522701149	G -> C	LOC_Os05g38700.1	downstream_gene_variant ; 298.0bp to feature; MODIFIER	silent_mutation	Average:57.252; most accessible tissue: Callus, score: 91.255	N	N	N	N
vg0522701149	G -> C	LOC_Os05g38690-LOC_Os05g38700	intergenic_region ; MODIFIER	silent_mutation	Average:57.252; most accessible tissue: Callus, score: 91.255	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0522701149	5.65E-06	5.65E-06	mr1419	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
vg0522701149	1.24E-06	1.06E-08	mr1901	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