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Detailed information for vg0716888581:

Variant ID: vg0716888581 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16888581
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

CTACAAAATTTTAGTTTTCCATTTCGATTGCTTCATGTTACATTCAGCTTACTTCTTTTCAGGTTGATGAGGCTATTTGGGTTGCTCAAAAGGCTCTTCG[T/C]
GGAATAAGATCAGACTGGGAAGAAGCAACACCACTGATGAAAGGGTTGGGATTTAAACCTAAGCTTTTGATGTTTAAATCATGGATCTGGGCTTTTGCAA

Reverse complement sequence

TTGCAAAAGCCCAGATCCATGATTTAAACATCAAAAGCTTAGGTTTAAATCCCAACCCTTTCATCAGTGGTGTTGCTTCTTCCCAGTCTGATCTTATTCC[A/G]
CGAAGAGCCTTTTGAGCAACCCAAATAGCCTCATCAACCTGAAAAGAAGTAAGCTGAATGTAACATGAAGCAATCGAAATGGAAAACTAAAATTTTGTAG

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	70.40%	28.80%	0.83%	0.00%	NA
All Indica	2759	97.20%	2.60%	0.22%	0.00%	NA
All Japonica	1512	20.20%	77.80%	2.05%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	95.50%	4.50%	0.00%	0.00%	NA
Indica Intermediate	786	96.40%	3.20%	0.38%	0.00%	NA
Temperate Japonica	767	19.30%	77.70%	3.00%	0.00%	NA
Tropical Japonica	504	22.20%	77.20%	0.60%	0.00%	NA
Japonica Intermediate	241	18.70%	79.30%	2.07%	0.00%	NA
VI/Aromatic	96	17.70%	82.30%	0.00%	0.00%	NA
Intermediate	90	61.10%	37.80%	1.11%	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
vg0716888581	T -> C	LOC_Os07g28840.1	synonymous_variant ; p.Arg148Arg; LOW	synonymous_codon	Average:48.61; most accessible tissue: Zhenshan97 young leaf, score: 63.096	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716888581	9.07E-06	NA	mr1204	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
vg0716888581	NA	1.39E-15	mr1842	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
vg0716888581	NA	2.71E-06	mr1020_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
vg0716888581	NA	1.43E-12	mr1128_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
vg0716888581	NA	1.93E-09	mr1506_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
vg0716888581	4.16E-06	NA	mr1567_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
vg0716888581	3.81E-07	4.16E-10	mr1806_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
vg0716888581	1.25E-07	1.25E-07	mr1806_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