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Detailed information for vg0609837969:

Variant ID: vg0609837969 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9837969
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, T: 0.06, A: 0.01, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

TGTGCCGAAGAAGCCGAGAGGATTCAGATCCTGGTCATTTTAAAAAAAATTATTTTACAAAATGACCACTGAAAAACTAATTCTAAAAAAAATTCTTTTT[T/G]
GCGCATCGGAGTGCCTGGTACCGTCGTTTAATAAGGCGGTGCCATCACCTCTCACGCTGTCCACATGCCAACGTGGCACCATGGGGGCCAACCGACGTTG

Reverse complement sequence

CAACGTCGGTTGGCCCCCATGGTGCCACGTTGGCATGTGGACAGCGTGAGAGGTGATGGCACCGCCTTATTAAACGACGGTACCAGGCACTCCGATGCGC[A/C]
AAAAAGAATTTTTTTTAGAATTAGTTTTTCAGTGGTCATTTTGTAAAATAATTTTTTTTAAAATGACCAGGATCTGAATCCTCTCGGCTTCTTCGGCACA

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%	13.10%	0.40%	34.28%	NA
All Indica	2759	74.60%	8.00%	0.36%	17.00%	NA
All Japonica	1512	20.40%	25.80%	0.53%	53.24%	NA
Aus	269	15.20%	0.00%	0.00%	84.76%	NA
Indica I	595	93.90%	4.70%	0.34%	1.01%	NA
Indica II	465	74.60%	8.80%	0.00%	16.56%	NA
Indica III	913	60.60%	12.80%	0.44%	26.18%	NA
Indica Intermediate	786	76.20%	4.60%	0.51%	18.70%	NA
Temperate Japonica	767	11.30%	47.30%	0.52%	40.81%	NA
Tropical Japonica	504	36.10%	1.60%	0.60%	61.71%	NA
Japonica Intermediate	241	16.60%	7.90%	0.41%	75.10%	NA
VI/Aromatic	96	7.30%	1.00%	1.04%	90.62%	NA
Intermediate	90	56.70%	8.90%	0.00%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609837969	T -> G	LOC_Os06g16960.1	upstream_gene_variant ; 3378.0bp to feature; MODIFIER	silent_mutation	Average:73.313; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N
vg0609837969	T -> G	LOC_Os06g16980.1	downstream_gene_variant ; 2920.0bp to feature; MODIFIER	silent_mutation	Average:73.313; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N
vg0609837969	T -> G	LOC_Os06g16980.2	downstream_gene_variant ; 2919.0bp to feature; MODIFIER	silent_mutation	Average:73.313; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N
vg0609837969	T -> G	LOC_Os06g16970.1	intron_variant ; MODIFIER	silent_mutation	Average:73.313; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N
vg0609837969	T -> DEL	N	N	silent_mutation	Average:73.313; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609837969	1.06E-06	NA	mr1695	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
vg0609837969	5.79E-06	NA	mr1695_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