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Detailed information for vg0608480356:

Variant ID: vg0608480356 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8480356
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.01, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTTGAAATTAGAGATAATGTGACTGAAAAGTTGTGTGTGTATGACAGGTTGATGTGATGGAAAAGGACTGAAGTTTAGATCCAAACTTTGGATCTAAA[C/G]
ACAGTCTAGGTGTTATAGTACCTAGGTATATGCATATAATTGAAACAGTTATATAAAAAATTTATAAAATTTGATATGATAAATTATGATAATATAAGAT

Reverse complement sequence

ATCTTATATTATCATAATTTATCATATCAAATTTTATAAATTTTTTATATAACTGTTTCAATTATATGCATATACCTAGGTACTATAACACCTAGACTGT[G/C]
TTTAGATCCAAAGTTTGGATCTAAACTTCAGTCCTTTTCCATCACATCAACCTGTCATACACACACAACTTTTCAGTCACATTATCTCTAATTTCAACTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.90%	31.10%	3.39%	22.62%	NA
All Indica	2759	5.50%	51.80%	5.51%	37.15%	NA
All Japonica	1512	99.00%	0.80%	0.13%	0.07%	NA
Aus	269	86.20%	0.70%	0.00%	13.01%	NA
Indica I	595	5.90%	50.40%	8.74%	34.96%	NA
Indica II	465	6.00%	57.00%	9.03%	27.96%	NA
Indica III	913	4.50%	42.30%	1.64%	51.59%	NA
Indica Intermediate	786	6.10%	60.90%	5.47%	27.48%	NA
Temperate Japonica	767	99.00%	0.80%	0.26%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	56.70%	30.00%	6.67%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608480356	C -> G	LOC_Os06g14940.1	upstream_gene_variant ; 1842.0bp to feature; MODIFIER	silent_mutation	Average:39.09; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N
vg0608480356	C -> G	LOC_Os06g14950.1	upstream_gene_variant ; 4622.0bp to feature; MODIFIER	silent_mutation	Average:39.09; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N
vg0608480356	C -> G	LOC_Os06g14930-LOC_Os06g14940	intergenic_region ; MODIFIER	silent_mutation	Average:39.09; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N
vg0608480356	C -> DEL	N	N	silent_mutation	Average:39.09; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608480356	NA	6.81E-46	mr1111	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
vg0608480356	NA	5.27E-31	mr1224	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
vg0608480356	9.73E-06	NA	mr1224	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
vg0608480356	NA	4.39E-09	mr1663	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
vg0608480356	NA	3.08E-06	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