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Detailed information for vg0408196898:

Variant ID: vg0408196898 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8196898
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCGATTTAATCATGCTGGCACCAGTACTACTCATCCCCTTTAATGGTGACATTGTACCGTGCTTATAGTAGGTCTTAAGTATTCTGGTTTTATTTTAT[T/C]
CACTTGTCCAAACTGATTTTTCTCTGTTCAAAAGTTAAATTCAAAAAGAAAAATATATAAAATAGTTTTGTATGTGTCTTTTCCTTTATTTTCTTTTCGT

Reverse complement sequence

ACGAAAAGAAAATAAAGGAAAAGACACATACAAAACTATTTTATATATTTTTCTTTTTGAATTTAACTTTTGAACAGAGAAAAATCAGTTTGGACAAGTG[A/G]
ATAAAATAAAACCAGAATACTTAAGACCTACTATAAGCACGGTACAATGTCACCATTAAAGGGGATGAGTAGTACTGGTGCCAGCATGATTAAATCGATA

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	72.90%	3.50%	7.49%	16.12%	NA
All Indica	2759	61.80%	5.60%	11.71%	20.84%	NA
All Japonica	1512	89.60%	0.30%	0.60%	9.46%	NA
Aus	269	86.20%	0.70%	4.83%	8.18%	NA
Indica I	595	66.10%	2.90%	10.76%	20.34%	NA
Indica II	465	59.10%	8.00%	13.12%	19.78%	NA
Indica III	913	60.60%	6.50%	11.61%	21.36%	NA
Indica Intermediate	786	61.70%	5.30%	11.70%	21.25%	NA
Temperate Japonica	767	98.40%	0.00%	0.00%	1.56%	NA
Tropical Japonica	504	76.20%	0.40%	0.60%	22.82%	NA
Japonica Intermediate	241	89.60%	1.20%	2.49%	6.64%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	73.30%	2.20%	10.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408196898	T -> C	LOC_Os04g14600.1	upstream_gene_variant ; 3348.0bp to feature; MODIFIER	silent_mutation	Average:23.031; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0408196898	T -> C	LOC_Os04g14610.1	upstream_gene_variant ; 194.0bp to feature; MODIFIER	silent_mutation	Average:23.031; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0408196898	T -> C	LOC_Os04g14620.1	upstream_gene_variant ; 1248.0bp to feature; MODIFIER	silent_mutation	Average:23.031; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0408196898	T -> C	LOC_Os04g14600-LOC_Os04g14610	intergenic_region ; MODIFIER	silent_mutation	Average:23.031; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0408196898	T -> DEL	N	N	silent_mutation	Average:23.031; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408196898	2.83E-06	NA	mr1676_2	Jap_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