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Detailed information for vg0810067400:

Variant ID: vg0810067400 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10067400
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTGCCGCCCATACAGAGGGCGGCAAGGGGCTAATTGCAATTTTGGCCGCCCATAAAGAGCTTGCGGCCGTACTTTTTGCATCTGGGTCCCTTGCCGCCC[T/C]
AATATGTAAAAAGTACGGCCAAAAGATTTTTCTATGTTATGTTAATAATAAATAAAGAAGTATTTATTGGTAAAACTTGTTAATATTGTTATAAAAATGT

Reverse complement sequence

ACATTTTTATAACAATATTAACAAGTTTTACCAATAAATACTTCTTTATTTATTATTAACATAACATAGAAAAATCTTTTGGCCGTACTTTTTACATATT[A/G]
GGGCGGCAAGGGACCCAGATGCAAAAAGTACGGCCGCAAGCTCTTTATGGGCGGCCAAAATTGCAATTAGCCCCTTGCCGCCCTCTGTATGGGCGGCAAG

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	32.10%	0.50%	0.80%	66.53%	NA
All Indica	2759	24.80%	0.70%	1.09%	73.36%	NA
All Japonica	1512	52.10%	0.00%	0.20%	47.75%	NA
Aus	269	3.70%	0.70%	0.37%	95.17%	NA
Indica I	595	16.60%	1.20%	0.84%	81.34%	NA
Indica II	465	39.10%	0.90%	0.86%	59.14%	NA
Indica III	913	25.60%	0.20%	1.20%	72.95%	NA
Indica Intermediate	786	21.60%	0.90%	1.27%	76.21%	NA
Temperate Japonica	767	87.20%	0.00%	0.00%	12.78%	NA
Tropical Japonica	504	8.90%	0.00%	0.60%	90.48%	NA
Japonica Intermediate	241	30.30%	0.00%	0.00%	69.71%	NA
VI/Aromatic	96	3.10%	3.10%	3.12%	90.62%	NA
Intermediate	90	37.80%	0.00%	1.11%	61.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0810067400	T -> C	LOC_Os08g16450.1	upstream_gene_variant ; 4463.0bp to feature; MODIFIER	silent_mutation	Average:31.377; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0810067400	T -> C	LOC_Os08g16440.1	downstream_gene_variant ; 869.0bp to feature; MODIFIER	silent_mutation	Average:31.377; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0810067400	T -> C	LOC_Os08g16430-LOC_Os08g16440	intergenic_region ; MODIFIER	silent_mutation	Average:31.377; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0810067400	T -> DEL	N	N	silent_mutation	Average:31.377; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810067400	NA	1.83E-06	mr1063	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
vg0810067400	NA	2.47E-12	mr1069	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
vg0810067400	NA	2.75E-06	mr1069	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
vg0810067400	NA	1.36E-06	mr1072	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
vg0810067400	NA	6.27E-07	mr1075	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
vg0810067400	NA	9.81E-09	mr1183	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
vg0810067400	5.26E-06	8.22E-08	mr1202	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
vg0810067400	NA	2.95E-13	mr1441	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
vg0810067400	NA	1.98E-07	mr1441	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
vg0810067400	NA	6.69E-08	mr1503	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
vg0810067400	NA	7.66E-09	mr1510	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
vg0810067400	4.71E-06	4.71E-06	mr1562	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