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Detailed information for vg0320639721:

Variant ID: vg0320639721 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20639721
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAAAATATGATCTTGCTTTCCTGTTGAATCAATTAACAATGAAAGATATTACACCCAGGAATTTGCTTTGATGAAGTCGGATCCCCCAATCGCTCAACG[T/C]
CGATCTCCCCGCCACCAAACTGGGCAAGGGAGCGGAGGACCAAGAATTCGGTCTGAACCTCAACCAAGTGCTTCTGATCCAGTCGGCCAGTCAGACTCTC

Reverse complement sequence

GAGAGTCTGACTGGCCGACTGGATCAGAAGCACTTGGTTGAGGTTCAGACCGAATTCTTGGTCCTCCGCTCCCTTGCCCAGTTTGGTGGCGGGGAGATCG[A/G]
CGTTGAGCGATTGGGGGATCCGACTTCATCAAAGCAAATTCCTGGGTGTAATATCTTTCATTGTTAATTGATTCAACAGGAAAGCAAGATCATATTTTGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.50%	32.40%	0.11%	0.00%	NA
All Indica	2759	97.40%	2.50%	0.07%	0.00%	NA
All Japonica	1512	12.70%	87.20%	0.07%	0.00%	NA
Aus	269	88.80%	11.20%	0.00%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	95.40%	4.30%	0.25%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	33.90%	65.90%	0.20%	0.00%	NA
Japonica Intermediate	241	7.90%	92.10%	0.00%	0.00%	NA
VI/Aromatic	96	27.10%	72.90%	0.00%	0.00%	NA
Intermediate	90	47.80%	50.00%	2.22%	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
vg0320639721	T -> C	LOC_Os03g37240.1	synonymous_variant ; p.Arg299Arg; LOW	synonymous_codon	Average:43.148; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320639721	NA	6.14E-08	mr1217	Jap_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
vg0320639721	1.12E-06	2.18E-09	mr1718	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
vg0320639721	NA	1.21E-07	mr1750	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
vg0320639721	NA	5.84E-06	mr1830	Jap_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
vg0320639721	NA	2.45E-07	mr1845	Jap_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