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Detailed information for vg1213226496:

Variant ID: vg1213226496 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13226496
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

ACCATGCTTTCCTTGTGTCGCTACTTTGTGGGTCTGGTCGCTTAGGAGGGTTCGCGTATTCCGCTGCGAGGACTTCCGCTTGAGCTTTCCTTTTCCCATT[T/C]
TTGCGATTTTTCTTCTTGCTTGACTCAGATGCGTTTGTGGCTGGTTTCTTCTCTCCCCCGGTCTTCGGCTTATCGTTCTTGCGTCTTAGCGCATCATCTG

Reverse complement sequence

CAGATGATGCGCTAAGACGCAAGAACGATAAGCCGAAGACCGGGGGAGAGAAGAAACCAGCCACAAACGCATCTGAGTCAAGCAAGAAGAAAAATCGCAA[A/G]
AATGGGAAAAGGAAAGCTCAAGCGGAAGTCCTCGCAGCGGAATACGCGAACCCTCCTAAGCGACCAGACCCACAAAGTAGCGACACAAGGAAAGCATGGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.40%	18.10%	10.43%	45.11%	NA
All Indica	2759	17.60%	28.70%	15.59%	38.17%	NA
All Japonica	1512	46.20%	0.50%	1.98%	51.39%	NA
Aus	269	10.00%	16.40%	8.18%	65.43%	NA
Indica I	595	12.10%	31.90%	21.34%	34.62%	NA
Indica II	465	16.10%	24.70%	16.77%	42.37%	NA
Indica III	913	23.50%	26.70%	11.06%	38.66%	NA
Indica Intermediate	786	15.60%	30.80%	15.78%	37.79%	NA
Temperate Japonica	767	79.00%	0.50%	0.78%	19.69%	NA
Tropical Japonica	504	4.80%	0.20%	3.57%	91.47%	NA
Japonica Intermediate	241	28.20%	0.80%	2.49%	68.46%	NA
VI/Aromatic	96	3.10%	2.10%	5.21%	89.58%	NA
Intermediate	90	37.80%	11.10%	6.67%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213226496	T -> C	LOC_Os12g23374.1	synonymous_variant ; p.Lys183Lys; LOW	synonymous_codon	Average:12.095; most accessible tissue: Callus, score: 58.003	N	N	N	N
vg1213226496	T -> DEL	LOC_Os12g23374.1	N	frameshift_variant	Average:12.095; most accessible tissue: Callus, score: 58.003	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213226496	NA	4.30E-06	mr1317_2	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
vg1213226496	1.29E-06	2.53E-09	mr1350_2	Jap_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