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Detailed information for vg0821623988:

Variant ID: vg0821623988 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 21623988
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.32, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GATCAGGGCGCCCGCGTAAACCGAACCGGATAAGTCGCGCGTAACCTATCCGGACTCCATGCCGTTTTCACGCACCGGATTTTTCGGAATGTTTCCAAAA[T/C]
AAAACAAATCCGAATTTCCCGTAGCAAAACAAAACTGCAAAAGGCAAAACAAAACAAATCCGAATTTCCCGCAGCAAAACAAAACTGCAAAAGGACGTTT

Reverse complement sequence

AAACGTCCTTTTGCAGTTTTGTTTTGCTGCGGGAAATTCGGATTTGTTTTGTTTTGCCTTTTGCAGTTTTGTTTTGCTACGGGAAATTCGGATTTGTTTT[A/G]
TTTTGGAAACATTCCGAAAAATCCGGTGCGTGAAAACGGCATGGAGTCCGGATAGGTTACGCGCGACTTATCCGGTTCGGTTTACGCGGGCGCCCTGATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.20%	15.40%	41.32%	0.00%	NA
All Indica	2759	21.80%	16.70%	61.54%	0.00%	NA
All Japonica	1512	83.50%	15.60%	0.86%	0.00%	NA
Aus	269	39.00%	5.60%	55.39%	0.00%	NA
Indica I	595	19.80%	8.40%	71.76%	0.00%	NA
Indica II	465	18.70%	29.00%	52.26%	0.00%	NA
Indica III	913	23.40%	15.60%	61.01%	0.00%	NA
Indica Intermediate	786	23.20%	16.90%	59.92%	0.00%	NA
Temperate Japonica	767	99.00%	0.80%	0.26%	0.00%	NA
Tropical Japonica	504	63.90%	35.30%	0.79%	0.00%	NA
Japonica Intermediate	241	75.50%	21.60%	2.90%	0.00%	NA
VI/Aromatic	96	27.10%	6.20%	66.67%	0.00%	NA
Intermediate	90	53.30%	14.40%	32.22%	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
vg0821623988	T -> C	LOC_Os08g34440.1	upstream_gene_variant ; 638.0bp to feature; MODIFIER	silent_mutation	Average:22.962; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0821623988	T -> C	LOC_Os08g34460.1	upstream_gene_variant ; 3056.0bp to feature; MODIFIER	silent_mutation	Average:22.962; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0821623988	T -> C	LOC_Os08g34450.1	downstream_gene_variant ; 738.0bp to feature; MODIFIER	silent_mutation	Average:22.962; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0821623988	T -> C	LOC_Os08g34440-LOC_Os08g34450	intergenic_region ; MODIFIER	silent_mutation	Average:22.962; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0821623988	1.84E-06	1.84E-06	mr1659	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