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Detailed information for vg1213036073:

Variant ID: vg1213036073 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13036073
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAACTATGTGCCTCGATCAGATATAATCCTCTTAGGTACACCATGAAGACATACTATCCTGGTCATGTATAACTCGGCTAGCTTGGCACTGCTGTAATT[T/C]
GTCTTAACAGGGATGAACCTCGCCATCTTGGTGAGTCGATCCACGATCACCTAAATGGAATCATATCCTGTTGCGGTCTTGGGCAATCCAACAATAAAAT

Reverse complement sequence

ATTTTATTGTTGGATTGCCCAAGACCGCAACAGGATATGATTCCATTTAGGTGATCGTGGATCGACTCACCAAGATGGCGAGGTTCATCCCTGTTAAGAC[A/G]
AATTACAGCAGTGCCAAGCTAGCCGAGTTATACATGACCAGGATAGTATGTCTTCATGGTGTACCTAAGAGGATTATATCTGATCGAGGCACATAGTTTA

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	17.60%	0.20%	24.02%	58.17%	NA
All Indica	2759	5.10%	0.20%	34.72%	59.99%	NA
All Japonica	1512	43.80%	0.20%	0.73%	55.22%	NA
Aus	269	0.40%	0.00%	49.07%	50.56%	NA
Indica I	595	3.70%	0.00%	8.91%	87.39%	NA
Indica II	465	4.50%	0.40%	38.71%	56.34%	NA
Indica III	913	4.20%	0.00%	51.15%	44.69%	NA
Indica Intermediate	786	7.60%	0.40%	32.82%	59.16%	NA
Temperate Japonica	767	78.50%	0.00%	0.13%	21.38%	NA
Tropical Japonica	504	0.80%	0.60%	1.59%	97.02%	NA
Japonica Intermediate	241	23.70%	0.00%	0.83%	75.52%	NA
VI/Aromatic	96	2.10%	0.00%	15.62%	82.29%	NA
Intermediate	90	26.70%	3.30%	21.11%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213036073	T -> C	LOC_Os12g23060.1	synonymous_variant ; p.Thr760Thr; LOW	synonymous_codon	Average:7.731; most accessible tissue: Callus, score: 31.143	N	N	N	N
vg1213036073	T -> DEL	LOC_Os12g23060.1	N	frameshift_variant	Average:7.731; most accessible tissue: Callus, score: 31.143	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213036073	NA	4.31E-12	mr1232	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
vg1213036073	3.29E-06	1.88E-08	mr1232	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
vg1213036073	NA	2.04E-06	mr1062_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
vg1213036073	NA	1.50E-06	mr1706_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
vg1213036073	6.64E-06	6.99E-08	mr1949_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