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Detailed information for vg0119128220:

Variant ID: vg0119128220 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19128220
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, T: 0.07, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGGTTGTTCTAGCCAAGAGTCAAGTACATTGCTTCCACTGTAGAGCTAGTGTGGCACTTGATCATCTCCGAGCCGGGTCATCGCTTATTACTCTTGGA[G/T]
GTTGCCGTCTACTAGACGGCTTGTGGAGGTGTTGCCCGGTGACCTCTCCGAGGAGATTGTGGAGGAGGCCCAGCGCCGGTTTGTGAGTGGTTTGGAGTTC

Reverse complement sequence

GAACTCCAAACCACTCACAAACCGGCGCTGGGCCTCCTCCACAATCTCCTCGGAGAGGTCACCGGGCAACACCTCCACAAGCCGTCTAGTAGACGGCAAC[C/A]
TCCAAGAGTAATAAGCGATGACCCGGCTCGGAGATGATCAAGTGCCACACTAGCTCTACAGTGGAAGCAATGTACTTGACTCTTGGCTAGAACAACCCTC

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	56.00%	17.00%	0.91%	26.07%	NA
All Indica	2759	26.50%	28.90%	1.49%	43.06%	NA
All Japonica	1512	97.90%	0.00%	0.13%	1.98%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	6.10%	79.20%	0.34%	14.45%	NA
Indica II	465	43.20%	10.30%	1.51%	44.95%	NA
Indica III	913	28.80%	6.80%	2.08%	62.32%	NA
Indica Intermediate	786	29.50%	27.60%	1.65%	41.22%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	95.20%	0.00%	0.40%	4.37%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	77.80%	6.70%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119128220	G -> T	LOC_Os01g34690.1	downstream_gene_variant ; 1748.0bp to feature; MODIFIER	silent_mutation	Average:44.231; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0119128220	G -> T	LOC_Os01g34680.1	intron_variant ; MODIFIER	silent_mutation	Average:44.231; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0119128220	G -> DEL	N	N	silent_mutation	Average:44.231; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119128220	NA	1.05E-07	mr1188	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
vg0119128220	NA	4.53E-08	mr1124_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
vg0119128220	NA	4.57E-06	mr1188_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
vg0119128220	7.22E-06	NA	mr1448_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
vg0119128220	2.79E-07	1.83E-11	mr1448_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
vg0119128220	NA	4.86E-06	mr1910_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