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Detailed information for vg0620931744:

Variant ID: vg0620931744 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20931744
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, G: 0.17, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

CACATGGAAAAATGATGGGGCCTCGTACAGAAAAATCACTTTTGTAGTAGTGTCACTCGCAGCCAGAGGAAGCCCTTCACCTGATGAGCTTGTTGCAAGA[T/G]
AGCGCCAGAAATGACAAGCTTTTAGATATGATTGACCACAGGATGGATGACATGCAGCTTCATTCTTAAGATGTAATGCACATGATGCATCTCGCAATGT

Reverse complement sequence

ACATTGCGAGATGCATCATGTGCATTACATCTTAAGAATGAAGCTGCATGTCATCCATCCTGTGGTCAATCATATCTAAAAGCTTGTCATTTCTGGCGCT[A/C]
TCTTGCAACAAGCTCATCAGGTGAAGGGCTTCCTCTGGCTGCGAGTGACACTACTACAAAAGTGATTTTTCTGTACGAGGCCCCATCATTTTTCCATGTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.20%	47.60%	0.17%	0.00%	NA
All Indica	2759	73.80%	25.90%	0.25%	0.00%	NA
All Japonica	1512	3.10%	96.80%	0.07%	0.00%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	95.30%	4.70%	0.00%	0.00%	NA
Indica II	465	67.50%	31.80%	0.65%	0.00%	NA
Indica III	913	57.70%	42.10%	0.22%	0.00%	NA
Indica Intermediate	786	80.00%	19.70%	0.25%	0.00%	NA
Temperate Japonica	767	1.60%	98.30%	0.13%	0.00%	NA
Tropical Japonica	504	6.00%	94.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	43.30%	56.70%	0.00%	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
vg0620931744	T -> G	LOC_Os06g35880.1	missense_variant ; p.Tyr162Ser; MODERATE	nonsynonymous_codon ; Y162S	Average:62.756; most accessible tissue: Minghui63 panicle, score: 74.563	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620931744	NA	1.67E-12	mr1216_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
vg0620931744	NA	3.38E-06	mr1549_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
vg0620931744	NA	8.18E-09	mr1582_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
vg0620931744	NA	9.69E-06	mr1609_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
vg0620931744	NA	1.17E-07	mr1623_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
vg0620931744	4.71E-06	4.71E-06	mr1666_2	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
vg0620931744	NA	3.25E-06	mr1734_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
vg0620931744	NA	1.14E-06	mr1761_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