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Detailed information for vg0101263892:

Variant ID: vg0101263892 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1263892
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

CCCGTCACTGGCTGCGCCCCCTCGATCGGTTAGGGTTTATGGGGTGGAGTGGCGGCGGCGGCGACGAACCTCGTTCCTTGTGTCGTTATGCCGTCCCGTC[T/C]
TCCACCCCTCTTTATATGGCACAGTGTGACGGGGGCCCACCAGCCATTGGGCTGGGCGCCCCCGATCAGGGCGCGGGTCAAGGCCCCCTTGAGCCGTTGG

Reverse complement sequence

CCAACGGCTCAAGGGGGCCTTGACCCGCGCCCTGATCGGGGGCGCCCAGCCCAATGGCTGGTGGGCCCCCGTCACACTGTGCCATATAAAGAGGGGTGGA[A/G]
GACGGGACGGCATAACGACACAAGGAACGAGGTTCGTCGCCGCCGCCGCCACTCCACCCCATAAACCCTAACCGATCGAGGGGGCGCAGCCAGTGACGGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.50%	7.00%	8.00%	26.51%	NA
All Indica	2759	59.20%	2.70%	6.42%	31.71%	NA
All Japonica	1512	64.90%	16.50%	12.10%	6.42%	NA
Aus	269	8.60%	0.40%	1.49%	89.59%	NA
Indica I	595	51.30%	5.90%	17.14%	25.71%	NA
Indica II	465	84.30%	3.90%	6.67%	5.16%	NA
Indica III	913	51.40%	0.30%	0.88%	47.43%	NA
Indica Intermediate	786	59.30%	2.40%	4.58%	33.72%	NA
Temperate Japonica	767	44.20%	28.00%	15.91%	11.86%	NA
Tropical Japonica	504	91.90%	0.60%	6.55%	0.99%	NA
Japonica Intermediate	241	74.70%	13.30%	11.62%	0.41%	NA
VI/Aromatic	96	76.00%	0.00%	3.12%	20.83%	NA
Intermediate	90	58.90%	6.70%	12.22%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0101263892	T -> DEL	N	N	silent_mutation	Average:52.285; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0101263892	T -> C	LOC_Os01g03200.1	upstream_gene_variant ; 1809.0bp to feature; MODIFIER	silent_mutation	Average:52.285; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0101263892	T -> C	LOC_Os01g03210.1	upstream_gene_variant ; 464.0bp to feature; MODIFIER	silent_mutation	Average:52.285; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0101263892	T -> C	LOC_Os01g03200-LOC_Os01g03210	intergenic_region ; MODIFIER	silent_mutation	Average:52.285; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101263892	2.83E-06	2.83E-06	mr1081_2	Jap_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