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Detailed information for vg0724212519:

Variant ID: vg0724212519 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24212519
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, A: 0.31, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GGTGACGTGCGGTGCGGAGGGCCTACCATGTATCGTCCAGTTCTAGTGGTTCTTCAGTAGTTTCCTAGCTAACTTTCGGGTCCTTAGTTATCATCAGACA[T/A]
AGGTGTCTATCGTCTATCAGTATTTTAGTGTTCTAGCTTTATTATCCATGTAACTCTGGAGTGATGAGGGAACAGCATGTCGATCCTGGCATCTTCAGGT

Reverse complement sequence

ACCTGAAGATGCCAGGATCGACATGCTGTTCCCTCATCACTCCAGAGTTACATGGATAATAAAGCTAGAACACTAAAATACTGATAGACGATAGACACCT[A/T]
TGTCTGATGATAACTAAGGACCCGAAAGTTAGCTAGGAAACTACTGAAGAACCACTAGAACTGGACGATACATGGTAGGCCCTCCGCACCGCACGTCACC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.10%	41.50%	0.08%	0.34%	NA
All Indica	2759	91.80%	7.80%	0.07%	0.33%	NA
All Japonica	1512	0.70%	99.10%	0.00%	0.20%	NA
Aus	269	44.60%	55.40%	0.00%	0.00%	NA
Indica I	595	93.10%	6.40%	0.17%	0.34%	NA
Indica II	465	87.70%	11.80%	0.00%	0.43%	NA
Indica III	913	97.00%	2.70%	0.00%	0.22%	NA
Indica Intermediate	786	87.30%	12.20%	0.13%	0.38%	NA
Temperate Japonica	767	0.70%	99.20%	0.00%	0.13%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	97.50%	0.00%	0.83%	NA
VI/Aromatic	96	44.80%	54.20%	0.00%	1.04%	NA
Intermediate	90	42.20%	52.20%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0724212519	T -> DEL	N	N	silent_mutation	Average:77.868; most accessible tissue: Callus, score: 99.911	N	N	N	N
vg0724212519	T -> A	LOC_Os07g40380.1	3_prime_UTR_variant ; 175.0bp to feature; MODIFIER	silent_mutation	Average:77.868; most accessible tissue: Callus, score: 99.911	N	N	N	N
vg0724212519	T -> A	LOC_Os07g40370.1	upstream_gene_variant ; 4554.0bp to feature; MODIFIER	silent_mutation	Average:77.868; most accessible tissue: Callus, score: 99.911	N	N	N	N
vg0724212519	T -> A	LOC_Os07g40390.1	downstream_gene_variant ; 3359.0bp to feature; MODIFIER	silent_mutation	Average:77.868; most accessible tissue: Callus, score: 99.911	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724212519	NA	9.69E-07	mr1082	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
vg0724212519	NA	2.91E-27	mr1181	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
vg0724212519	NA	1.13E-31	mr1213	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
vg0724212519	NA	8.88E-07	mr1408	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
vg0724212519	NA	2.55E-07	mr1761	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
vg0724212519	NA	8.13E-33	mr1878	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
vg0724212519	NA	2.24E-06	mr1181_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
vg0724212519	NA	1.66E-08	mr1319_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