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Detailed information for vg0143171338:

Variant ID: vg0143171338 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 43171338
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.06, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCAGATTTGAAAATTTTGAAAACTTACATCTTGAAATTTGAAAATTTTTAACTTGAGATTTGAAAACTTTCAACTCGAGATTCAAAAACTTTCAAGTT[T/C]
AGATTTGAAAATTTTGAAAACTTTCAACTTGAGATTTGAAAAATTTTAAACTCAAGATTTGAAAACTTTCAAATCCAGATTTAAAAACTTTCACCTCGAG

Reverse complement sequence

CTCGAGGTGAAAGTTTTTAAATCTGGATTTGAAAGTTTTCAAATCTTGAGTTTAAAATTTTTCAAATCTCAAGTTGAAAGTTTTCAAAATTTTCAAATCT[A/G]
AACTTGAAAGTTTTTGAATCTCGAGTTGAAAGTTTTCAAATCTCAAGTTAAAAATTTTCAAATTTCAAGATGTAAGTTTTCAAAATTTTCAAATCTGGAC

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	47.60%	15.50%	4.68%	32.29%	NA
All Indica	2759	20.60%	25.30%	5.44%	48.68%	NA
All Japonica	1512	98.30%	1.30%	0.00%	0.40%	NA
Aus	269	14.90%	1.10%	23.79%	60.22%	NA
Indica I	595	16.80%	0.20%	8.91%	74.12%	NA
Indica II	465	4.50%	68.60%	2.37%	24.52%	NA
Indica III	913	24.20%	22.50%	4.05%	49.29%	NA
Indica Intermediate	786	28.60%	22.10%	6.23%	43.00%	NA
Temperate Japonica	767	99.30%	0.40%	0.00%	0.26%	NA
Tropical Japonica	504	96.40%	3.20%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	96.90%	1.00%	1.04%	1.04%	NA
Intermediate	90	67.80%	10.00%	6.67%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0143171338	T -> DEL	N	N	silent_mutation	Average:19.121; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0143171338	T -> C	LOC_Os01g74530.2	upstream_gene_variant ; 4351.0bp to feature; MODIFIER	silent_mutation	Average:19.121; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0143171338	T -> C	LOC_Os01g74540.1	downstream_gene_variant ; 756.0bp to feature; MODIFIER	silent_mutation	Average:19.121; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0143171338	T -> C	LOC_Os01g74550.1	downstream_gene_variant ; 4109.0bp to feature; MODIFIER	silent_mutation	Average:19.121; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0143171338	T -> C	LOC_Os01g74530-LOC_Os01g74540	intergenic_region ; MODIFIER	silent_mutation	Average:19.121; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0143171338	NA	8.05E-08	mr1974_2	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
vg0143171338	3.36E-06	3.70E-08	mr1974_2	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