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Detailed information for vg0412166793:

Variant ID: vg0412166793 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12166793
Reference Allele: C	Alternative Allele: T
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: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TCAGACCGGCCAGGTTGAGTGGGCTCAATGATTGCCCTGTAACGGCTAGTTTTCTAGCCGTTACAAAGTAGTCCGGTCTGACCGGCCACTCTATGGCGGT[C/T]
TAACCGGCAGAGCACAGAGTTGGGGATTTCGACATAACGGCTAGTTTTGGTGGTTGGGGGTATATATACCCACTCCCCAGCAGCAAGGGTAAGGTTTTGG

Reverse complement sequence

CCAAAACCTTACCCTTGCTGCTGGGGAGTGGGTATATATACCCCCAACCACCAAAACTAGCCGTTATGTCGAAATCCCCAACTCTGTGCTCTGCCGGTTA[G/A]
ACCGCCATAGAGTGGCCGGTCAGACCGGACTACTTTGTAACGGCTAGAAAACTAGCCGTTACAGGGCAATCATTGAGCCCACTCAACCTGGCCGGTCTGA

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	42.90%	10.50%	39.82%	6.75%	NA
All Indica	2759	29.60%	17.20%	52.16%	1.05%	NA
All Japonica	1512	60.80%	0.70%	20.83%	17.59%	NA
Aus	269	72.10%	3.00%	24.91%	0.00%	NA
Indica I	595	10.60%	18.30%	69.58%	1.51%	NA
Indica II	465	30.80%	8.80%	58.71%	1.72%	NA
Indica III	913	41.10%	22.70%	35.60%	0.66%	NA
Indica Intermediate	786	29.90%	15.00%	54.33%	0.76%	NA
Temperate Japonica	767	82.00%	0.10%	9.26%	8.60%	NA
Tropical Japonica	504	33.90%	1.80%	37.70%	26.59%	NA
Japonica Intermediate	241	49.80%	0.40%	22.41%	27.39%	NA
VI/Aromatic	96	51.00%	1.00%	30.21%	17.71%	NA
Intermediate	90	53.30%	3.30%	35.56%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412166793	C -> DEL	N	N	silent_mutation	Average:30.979; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0412166793	C -> T	LOC_Os04g21520.1	upstream_gene_variant ; 4565.0bp to feature; MODIFIER	silent_mutation	Average:30.979; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0412166793	C -> T	LOC_Os04g21510.1	intron_variant ; MODIFIER	silent_mutation	Average:30.979; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412166793	8.82E-06	NA	mr1062	Ind_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
vg0412166793	4.03E-06	NA	mr1807	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