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Detailed information for vg1013346416:

Variant ID: vg1013346416 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13346416
Reference Allele: C	Alternative Allele: T
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: 254. )

Flanking Sequence (100 bp) in Reference Genome:

AACCTTCAATGATGCTCCCCTCGGGTTTAGCTCTGTTACGAACGTACGACTTCAGAACTCCCATGTACCTTTCAAACGGACACATTTCCCTTAGAAAAGC[C/T]
GGGCCACATAGTTTTGTTTGCTTCACCATATGAACAGGGAGATGAACCATTATATCAAAGAAAGACAGTGGGAAAAACATCTCCAGGTGACAGAGGGTAT

Reverse complement sequence

ATACCCTCTGTCACCTGGAGATGTTTTTCCCACTGTCTTTCTTTGATATAATGGTTCATCTCCCTGTTCATATGGTGAAGCAAACAAAACTATGTGGCCC[G/A]
GCTTTTCTAAGGGAAATGTGTCCGTTTGAAAGGTACATGGGAGTTCTGAAGTCGTACGTTCGTAACAGAGCTAAACCCGAGGGGAGCATCATTGAAGGTT

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	50.10%	49.50%	0.40%	0.00%	NA
All Indica	2759	26.20%	73.30%	0.51%	0.00%	NA
All Japonica	1512	99.30%	0.60%	0.07%	0.00%	NA
Aus	269	2.60%	96.30%	1.12%	0.00%	NA
Indica I	595	31.10%	68.10%	0.84%	0.00%	NA
Indica II	465	9.00%	91.00%	0.00%	0.00%	NA
Indica III	913	29.80%	69.80%	0.44%	0.00%	NA
Indica Intermediate	786	28.50%	70.90%	0.64%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	80.20%	19.80%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	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
vg1013346416	C -> T	LOC_Os10g25760.1	synonymous_variant ; p.Pro652Pro; LOW	synonymous_codon	Average:20.907; most accessible tissue: Minghui63 flower, score: 31.021	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013346416	NA	2.88E-08	mr1533	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
vg1013346416	5.98E-07	NA	mr1980	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
vg1013346416	6.87E-07	5.09E-11	mr1980	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
vg1013346416	7.15E-06	1.55E-10	mr1533_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