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Detailed information for vg1223866038:

Variant ID: vg1223866038 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23866038
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, A: 0.20, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TATCGTAGTGCTTTGCAAACAGGGCATGCTTCTAGGTTCTCGTACTCCTCACCGCAATATAGGATACAATCATTTGGACATGCGTGAATCTTCTGAACTT[A/C]
CAGTCCTAGAGGGCAGACTATCTTCTCAGCCTCGTACGTTGTCTCGGGCAATTTGTTTCTCTTCGGAAGAATGTTCTTGACGAGTCTCAATAAATCACCA

Reverse complement sequence

TGGTGATTTATTGAGACTCGTCAAGAACATTCTTCCGAAGAGAAACAAATTGCCCGAGACAACGTACGAGGCTGAGAAGATAGTCTGCCCTCTAGGACTG[T/G]
AAGTTCAGAAGATTCACGCATGTCCAAATGATTGTATCCTATATTGCGGTGAGGAGTACGAGAACCTAGAAGCATGCCCTGTTTGCAAAGCACTACGATA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	29.20%	3.50%	44.22%	23.11%	NA
All Indica	2759	3.30%	5.50%	58.72%	32.51%	NA
All Japonica	1512	76.30%	0.10%	11.71%	11.90%	NA
Aus	269	2.60%	3.00%	92.19%	2.23%	NA
Indica I	595	1.70%	4.90%	53.95%	39.50%	NA
Indica II	465	5.60%	3.40%	66.88%	24.09%	NA
Indica III	913	3.00%	7.90%	60.46%	28.70%	NA
Indica Intermediate	786	3.60%	4.30%	55.47%	36.64%	NA
Temperate Japonica	767	84.90%	0.00%	5.48%	9.65%	NA
Tropical Japonica	504	72.20%	0.20%	17.66%	9.92%	NA
Japonica Intermediate	241	57.70%	0.00%	19.09%	23.24%	NA
VI/Aromatic	96	88.50%	0.00%	11.46%	0.00%	NA
Intermediate	90	47.80%	4.40%	37.78%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223866038	A -> C	LOC_Os12g38840.1	N	splice_donor_variant	Average:10.204; most accessible tissue: Callus, score: 26.731	N	N	N	N
vg1223866038	A -> DEL	LOC_Os12g38840.1	N	splice_donor_variant	Average:10.204; most accessible tissue: Callus, score: 26.731	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223866038	NA	4.45E-16	mr1118	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
vg1223866038	NA	7.06E-19	mr1242	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
vg1223866038	NA	2.95E-06	mr1159_2	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
vg1223866038	NA	3.46E-09	mr1645_2	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
vg1223866038	9.00E-06	2.43E-08	mr1648_2	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
vg1223866038	NA	4.11E-06	mr1655_2	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
vg1223866038	3.02E-06	1.82E-22	mr1657_2	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
vg1223866038	NA	1.34E-11	mr1722_2	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
vg1223866038	NA	7.69E-06	mr1840_2	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