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Detailed information for vg0608915375:

Variant ID: vg0608915375 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8915375
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATCAACAGAAGGCTCTGGGTGCCGCAGCGTGAAGAAAAATACCCCGGAAGTCTTTAGAAATCAGCTATGCTTTATCCATATAAGTGATAGGTAAATT[G/T]
AAGCAGTTCCTTCTTGTCCTTATTAGTCAGCAGGCACTTTTTAAAGGGCTGCTCTACTTCGTGCAGCTTTGGGCAGATCGATATGCTCACGAACTGCATG

Reverse complement sequence

CATGCAGTTCGTGAGCATATCGATCTGCCCAAAGCTGCACGAAGTAGAGCAGCCCTTTAAAAAGTGCCTGCTGACTAATAAGGACAAGAAGGAACTGCTT[C/A]
AATTTACCTATCACTTATATGGATAAAGCATAGCTGATTTCTAAAGACTTCCGGGGTATTTTTCTTCACGCTGCGGCACCCAGAGCCTTCTGTTGATAAT

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	65.80%	33.90%	0.08%	0.25%	NA
All Indica	2759	43.00%	56.50%	0.11%	0.36%	NA
All Japonica	1512	99.00%	0.80%	0.07%	0.13%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	44.90%	55.00%	0.17%	0.00%	NA
Indica II	465	23.40%	75.50%	0.00%	1.08%	NA
Indica III	913	57.20%	42.70%	0.00%	0.11%	NA
Indica Intermediate	786	36.80%	62.50%	0.25%	0.51%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	0.60%	0.20%	0.20%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	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
vg0608915375	G -> T	LOC_Os06g15730.1	3_prime_UTR_variant ; 169.0bp to feature; MODIFIER	silent_mutation	Average:54.847; most accessible tissue: Minghui63 flag leaf, score: 80.786	N	N	N	N
vg0608915375	G -> DEL	N	N	silent_mutation	Average:54.847; most accessible tissue: Minghui63 flag leaf, score: 80.786	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608915375	NA	5.72E-09	mr1946	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
vg0608915375	NA	6.39E-07	mr1329_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
vg0608915375	NA	7.48E-09	mr1446_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
vg0608915375	NA	8.67E-07	mr1524_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
vg0608915375	NA	1.10E-18	mr1578_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
vg0608915375	NA	4.71E-08	mr1578_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
vg0608915375	NA	2.28E-09	mr1649_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
vg0608915375	NA	2.11E-06	mr1668_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
vg0608915375	NA	3.90E-08	mr1754_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
vg0608915375	NA	1.38E-08	mr1819_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
vg0608915375	NA	5.94E-07	mr1982_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