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Detailed information for vg0725097326:

Variant ID: vg0725097326 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 25097326
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTCCATTAGCTACCATGGGATTTTTTTTCCATTAGCTACCATGGGATAGATGCTAATCACGTTGGAGTGACTAGATGGGAACTAATATTTTATTGCT[T/A]
AATTATACTATAATATATGAGATTAATATTAATTGGAAAATTCCTGTGGTTTATATATTCCTGTGTTCCGAACGCTTCGTACTATCAAATTCTTTTGTTT

Reverse complement sequence

AAACAAAAGAATTTGATAGTACGAAGCGTTCGGAACACAGGAATATATAAACCACAGGAATTTTCCAATTAATATTAATCTCATATATTATAGTATAATT[A/T]
AGCAATAAAATATTAGTTCCCATCTAGTCACTCCAACGTGATTAGCATCTATCCCATGGTAGCTAATGGAAAAAAAATCCCATGGTAGCTAATGGAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.30%	14.60%	21.56%	14.58%	NA
All Indica	2759	41.00%	24.30%	34.11%	0.62%	NA
All Japonica	1512	55.40%	0.20%	1.79%	42.66%	NA
Aus	269	86.20%	4.50%	9.29%	0.00%	NA
Indica I	595	73.80%	3.50%	22.69%	0.00%	NA
Indica II	465	48.80%	8.60%	40.86%	1.72%	NA
Indica III	913	11.50%	53.30%	35.05%	0.11%	NA
Indica Intermediate	786	45.80%	15.50%	37.66%	1.02%	NA
Temperate Japonica	767	42.60%	0.10%	0.65%	56.58%	NA
Tropical Japonica	504	62.90%	0.40%	2.78%	33.93%	NA
Japonica Intermediate	241	80.10%	0.00%	3.32%	16.60%	NA
VI/Aromatic	96	83.30%	0.00%	6.25%	10.42%	NA
Intermediate	90	54.40%	4.40%	22.22%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0725097326	T -> DEL	N	N	silent_mutation	Average:35.643; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0725097326	T -> A	LOC_Os07g41880.1	upstream_gene_variant ; 2511.0bp to feature; MODIFIER	silent_mutation	Average:35.643; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0725097326	T -> A	LOC_Os07g41890.1	upstream_gene_variant ; 380.0bp to feature; MODIFIER	silent_mutation	Average:35.643; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0725097326	T -> A	LOC_Os07g41900.1	upstream_gene_variant ; 3074.0bp to feature; MODIFIER	silent_mutation	Average:35.643; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0725097326	T -> A	LOC_Os07g41880-LOC_Os07g41890	intergenic_region ; MODIFIER	silent_mutation	Average:35.643; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0725097326	NA	2.16E-09	mr1065	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
vg0725097326	NA	2.58E-10	mr1091	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
vg0725097326	4.60E-06	4.58E-06	mr1197_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
vg0725097326	2.10E-06	2.10E-06	mr1478_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
vg0725097326	NA	7.16E-08	mr1530_2	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
vg0725097326	NA	2.03E-07	mr1745_2	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
vg0725097326	NA	2.96E-07	mr1877_2	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