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Detailed information for vg0625665252:

Variant ID: vg0625665252 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 25665252
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.08, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGGACTAAAGATCCCGGGGGGGGGCTTGACAGGCCCTGACAGCATTTGAACCGGGACTAAAGATGATCTTCACCAACCGGGACTAAAGATCAAATATG[T/C]
CCGTTACCCTTTTTAACCGGGACTAAAGATCATCTTTAGCCCCAGTTTTTATTACATCCGGGTCTATTGTGGAATTCGGCCGACCGACGAAAGATAGTTT

Reverse complement sequence

AAACTATCTTTCGTCGGTCGGCCGAATTCCACAATAGACCCGGATGTAATAAAAACTGGGGCTAAAGATGATCTTTAGTCCCGGTTAAAAAGGGTAACGG[A/G]
CATATTTGATCTTTAGTCCCGGTTGGTGAAGATCATCTTTAGTCCCGGTTCAAATGCTGTCAGGGCCTGTCAAGCCCCCCCCCGGGATCTTTAGTCCTGG

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	63.80%	36.10%	0.06%	0.00%	NA
All Indica	2759	97.00%	3.00%	0.00%	0.00%	NA
All Japonica	1512	3.70%	96.10%	0.20%	0.00%	NA
Aus	269	81.40%	18.60%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	94.20%	5.80%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	93.80%	6.20%	0.00%	0.00%	NA
Temperate Japonica	767	3.80%	95.80%	0.39%	0.00%	NA
Tropical Japonica	504	5.20%	94.80%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	18.80%	81.20%	0.00%	0.00%	NA
Intermediate	90	51.10%	48.90%	0.00%	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
vg0625665252	T -> C	LOC_Os06g42680.1	downstream_gene_variant ; 4735.0bp to feature; MODIFIER	silent_mutation	Average:52.663; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0625665252	T -> C	LOC_Os06g42680.2	downstream_gene_variant ; 4735.0bp to feature; MODIFIER	silent_mutation	Average:52.663; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0625665252	T -> C	LOC_Os06g42670.1	intron_variant ; MODIFIER	silent_mutation	Average:52.663; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0625665252	1.93E-06	1.93E-06	mr1011	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