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Detailed information for vg0630627914:

Variant ID: vg0630627914 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 30627914
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, C: 0.07, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CGCATAGGGCGCCGTAGAGTGGTCGTGGACGCACGGGAGGGGCGTCGTGGACCAAGGTGCGCGAGGATGCACTGGAGACGAAGACGGTGACACAATCACG[G/C]
CAGTCGTTGAGGAAGATGACGCCGAAAAGCCGATGTAGTCGAACCGTGAAGGACGAGACGTCACACAGGGTGTCACGCCCCGAACCAGTCCCGACCGGAA

Reverse complement sequence

TTCCGGTCGGGACTGGTTCGGGGCGTGACACCCTGTGTGACGTCTCGTCCTTCACGGTTCGACTACATCGGCTTTTCGGCGTCATCTTCCTCAACGACTG[C/G]
CGTGATTGTGTCACCGTCTTCGTCTCCAGTGCATCCTCGCGCACCTTGGTCCACGACGCCCCTCCCGTGCGTCCACGACCACTCTACGGCGCCCTATGCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.70%	9.20%	1.46%	53.64%	NA
All Indica	2759	18.80%	10.40%	1.59%	69.16%	NA
All Japonica	1512	65.50%	0.40%	1.32%	32.80%	NA
Aus	269	41.60%	48.00%	1.12%	9.29%	NA
Indica I	595	1.80%	3.70%	1.68%	92.77%	NA
Indica II	465	20.90%	10.30%	2.37%	66.45%	NA
Indica III	913	29.20%	15.90%	0.88%	54.00%	NA
Indica Intermediate	786	18.30%	9.30%	1.91%	70.48%	NA
Temperate Japonica	767	82.90%	0.80%	0.65%	15.65%	NA
Tropical Japonica	504	43.30%	0.00%	1.79%	54.96%	NA
Japonica Intermediate	241	56.40%	0.00%	2.49%	41.08%	NA
VI/Aromatic	96	36.50%	0.00%	0.00%	63.54%	NA
Intermediate	90	35.60%	12.20%	2.22%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0630627914	G -> C	LOC_Os06g50600.1	upstream_gene_variant ; 3695.0bp to feature; MODIFIER	silent_mutation	Average:9.982; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0630627914	G -> C	LOC_Os06g50600.2	upstream_gene_variant ; 3695.0bp to feature; MODIFIER	silent_mutation	Average:9.982; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0630627914	G -> C	LOC_Os06g50600-LOC_Os06g50610	intergenic_region ; MODIFIER	silent_mutation	Average:9.982; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0630627914	G -> DEL	N	N	silent_mutation	Average:9.982; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0630627914	2.58E-06	2.58E-06	mr1473	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