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Detailed information for vg0429470009:

Variant ID: vg0429470009 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 29470009
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, C: 0.03, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

AACGTCAATGATTGTGCAGATATGACTCAAGTTCCAGCAAATGCAGAAGGAATTCGCAAGGAATACACCACCAAAGTGAATAGACAAGAATCAAGAACAG[G/C]
TATAAATTATTTTCTTGCCTGGTGAGAAGCAAAATTAAGATTTGCTTACATTATTTTCAGTCATTTAACAATTTTCAAACAAGTTACAGTGAAAGAATAA

Reverse complement sequence

TTATTCTTTCACTGTAACTTGTTTGAAAATTGTTAAATGACTGAAAATAATGTAAGCAAATCTTAATTTTGCTTCTCACCAGGCAAGAAAATAATTTATA[C/G]
CTGTTCTTGATTCTTGTCTATTCACTTTGGTGGTGTATTCCTTGCGAATTCCTTCTGCATTTGCTGGAACTTGAGTCATATCTGCACAATCATTGACGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.10%	45.90%	2.01%	0.02%	NA
All Indica	2759	85.30%	12.20%	2.43%	0.04%	NA
All Japonica	1512	0.50%	99.50%	0.00%	0.00%	NA
Aus	269	13.00%	78.10%	8.92%	0.00%	NA
Indica I	595	91.80%	6.10%	2.18%	0.00%	NA
Indica II	465	91.80%	6.20%	1.72%	0.22%	NA
Indica III	913	77.00%	19.10%	3.94%	0.00%	NA
Indica Intermediate	786	86.30%	12.50%	1.27%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	0.60%	99.40%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	35.40%	63.50%	1.04%	0.00%	NA
Intermediate	90	33.30%	63.30%	3.33%	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
vg0429470009	G -> C	LOC_Os04g49380.1	splice_donor_variant&intron_variant ; HIGH	splice_donor_variant	Average:14.023; most accessible tissue: Callus, score: 20.986	N	N	N	N
vg0429470009	G -> DEL	LOC_Os04g49380.1	N	splice_donor_variant	Average:14.023; most accessible tissue: Callus, score: 20.986	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0429470009	NA	9.86E-06	mr1030	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
vg0429470009	NA	2.97E-17	mr1253	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
vg0429470009	NA	6.01E-08	mr1648	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
vg0429470009	NA	1.12E-12	mr1663	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
vg0429470009	NA	4.77E-13	mr1819	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
vg0429470009	NA	2.54E-11	mr1938	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