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Detailed information for vg0512327313:

Variant ID: vg0512327313 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 12327313
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CATAAATTAAAATGATGCTAGACTTACTTTTCCTTGCTTATTTTACTCATAATTGCTCAATAAAATTAGCTTTATGCAAATGTTGAACCTAGAGACCCAC[C/T]
ATAGGCTAGAAAGCTTGCATACTTCTTTCTCCCTTATGTATATATAATTTTGGGTAAGACTTGCGAGTACAATCTTGTACTTAACCCGGTGTCTGCAATT

Reverse complement sequence

AATTGCAGACACCGGGTTAAGTACAAGATTGTACTCGCAAGTCTTACCCAAAATTATATATACATAAGGGAGAAAGAAGTATGCAAGCTTTCTAGCCTAT[G/A]
GTGGGTCTCTAGGTTCAACATTTGCATAAAGCTAATTTTATTGAGCAATTATGAGTAAAATAAGCAAGGAAAAGTAAGTCTAGCATCATTTTAATTTATG

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	73.10%	19.10%	7.72%	0.06%	NA
All Indica	2759	84.70%	5.30%	9.93%	0.11%	NA
All Japonica	1512	45.60%	49.20%	5.16%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	67.20%	12.40%	20.34%	0.00%	NA
Indica II	465	82.80%	4.90%	12.26%	0.00%	NA
Indica III	913	96.10%	0.40%	3.18%	0.33%	NA
Indica Intermediate	786	85.80%	5.70%	8.52%	0.00%	NA
Temperate Japonica	767	13.00%	82.00%	4.95%	0.00%	NA
Tropical Japonica	504	86.90%	9.10%	3.97%	0.00%	NA
Japonica Intermediate	241	63.10%	28.60%	8.30%	0.00%	NA
VI/Aromatic	96	94.80%	1.00%	4.17%	0.00%	NA
Intermediate	90	76.70%	15.60%	7.78%	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
vg0512327313	C -> T	LOC_Os05g20960.1	upstream_gene_variant ; 4709.0bp to feature; MODIFIER	silent_mutation	Average:51.219; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0512327313	C -> T	LOC_Os05g20950.1	downstream_gene_variant ; 4228.0bp to feature; MODIFIER	silent_mutation	Average:51.219; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0512327313	C -> T	LOC_Os05g20954.1	downstream_gene_variant ; 251.0bp to feature; MODIFIER	silent_mutation	Average:51.219; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0512327313	C -> T	LOC_Os05g20954.2	intron_variant ; MODIFIER	silent_mutation	Average:51.219; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0512327313	C -> T	LOC_Os05g20954.3	intron_variant ; MODIFIER	silent_mutation	Average:51.219; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0512327313	C -> T	LOC_Os05g20954.4	intron_variant ; MODIFIER	silent_mutation	Average:51.219; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0512327313	C -> DEL	N	N	silent_mutation	Average:51.219; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0512327313	2.10E-07	NA	mr1552	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
vg0512327313	3.14E-06	5.79E-13	mr1552	Jap_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
vg0512327313	NA	4.08E-06	mr1657	Jap_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
vg0512327313	NA	5.97E-08	mr1862	Jap_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