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Detailed information for vg0135567772:

Variant ID: vg0135567772 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 35567772
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.03, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

CCGGTCTGACCGGCCACCCCATGCCGGTCTGACCAGCCAGGCCGTTGGGGCCCTCTGACAGGGCTACAACAGCTAGTTTTCTAGCCGTTGCAGAGTAGCA[C/T]
GGTCTGACCGGCCACATACCTCCGATCAGACCGGCAGAGCACAGAGTTAGGGGATTTCGCCCCCAACGACTAGTTTTGGTGGGTGGGAGTATAAATACTC

Reverse complement sequence

GAGTATTTATACTCCCACCCACCAAAACTAGTCGTTGGGGGCGAAATCCCCTAACTCTGTGCTCTGCCGGTCTGATCGGAGGTATGTGGCCGGTCAGACC[G/A]
TGCTACTCTGCAACGGCTAGAAAACTAGCTGTTGTAGCCCTGTCAGAGGGCCCCAACGGCCTGGCTGGTCAGACCGGCATGGGGTGGCCGGTCAGACCGG

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	51.00%	36.60%	7.07%	5.31%	NA
All Indica	2759	82.00%	1.20%	7.94%	8.84%	NA
All Japonica	1512	1.50%	98.30%	0.13%	0.07%	NA
Aus	269	36.10%	22.70%	39.78%	1.49%	NA
Indica I	595	73.40%	0.70%	9.92%	15.97%	NA
Indica II	465	91.40%	0.90%	2.80%	4.95%	NA
Indica III	913	84.80%	1.00%	7.34%	6.90%	NA
Indica Intermediate	786	79.60%	2.20%	10.18%	8.02%	NA
Temperate Japonica	767	1.00%	98.80%	0.13%	0.00%	NA
Tropical Japonica	504	2.00%	97.80%	0.00%	0.20%	NA
Japonica Intermediate	241	1.70%	97.90%	0.41%	0.00%	NA
VI/Aromatic	96	2.10%	96.90%	1.04%	0.00%	NA
Intermediate	90	31.10%	61.10%	5.56%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0135567772	C -> T	LOC_Os01g61490.1	upstream_gene_variant ; 879.0bp to feature; MODIFIER	silent_mutation	Average:18.052; most accessible tissue: Callus, score: 24.739	N	N	N	N
vg0135567772	C -> T	LOC_Os01g61480-LOC_Os01g61490	intergenic_region ; MODIFIER	silent_mutation	Average:18.052; most accessible tissue: Callus, score: 24.739	N	N	N	N
vg0135567772	C -> DEL	N	N	silent_mutation	Average:18.052; most accessible tissue: Callus, score: 24.739	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0135567772	3.91E-06	NA	mr1015	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
vg0135567772	3.08E-06	NA	mr1015	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
vg0135567772	6.64E-06	NA	mr1116	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
vg0135567772	NA	8.39E-12	mr1553	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
vg0135567772	6.27E-06	2.66E-12	mr1623	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
vg0135567772	NA	1.82E-07	mr1781	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