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Detailed information for vg0913451651:

Variant ID: vg0913451651 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13451651
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, T: 0.20, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTGAGTTCAGAGATAATGTTAGACTTTCTTTATCAGCCTCGTGCGGGAACCTAAAGGGTTTGTCTGAGTCCATCTCCGACGTCAACCAAGAAAGTACA[G/T]
AACATACGACTAAGTCTCCTGTCTTGCTGTAATCGAGAATTTGGATTGAAGTCAAGAAATTTTATCTCGGCGGGTACACCATCTCTTCATTCTGTATTCC

Reverse complement sequence

GGAATACAGAATGAAGAGATGGTGTACCCGCCGAGATAAAATTTCTTGACTTCAATCCAAATTCTCGATTACAGCAAGACAGGAGACTTAGTCGTATGTT[C/A]
TGTACTTTCTTGGTTGACGTCGGAGATGGACTCAGACAAACCCTTTAGGTTCCCGCACGAGGCTGATAAAGAAAGTCTAACATTATCTCTGAACTCACAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.20%	31.90%	2.48%	0.51%	NA
All Indica	2759	95.90%	2.00%	2.07%	0.04%	NA
All Japonica	1512	9.70%	90.30%	0.00%	0.00%	NA
Aus	269	58.40%	17.50%	20.07%	4.09%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	91.80%	5.80%	2.15%	0.22%	NA
Indica III	913	96.20%	1.20%	2.63%	0.00%	NA
Indica Intermediate	786	95.50%	1.50%	2.93%	0.00%	NA
Temperate Japonica	767	5.20%	94.80%	0.00%	0.00%	NA
Tropical Japonica	504	17.70%	82.30%	0.00%	0.00%	NA
Japonica Intermediate	241	7.10%	92.90%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	1.00%	5.21%	12.50%	NA
Intermediate	90	57.80%	41.10%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0913451651	G -> DEL	N	N	silent_mutation	Average:51.068; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N
vg0913451651	G -> T	LOC_Os09g22230.1	upstream_gene_variant ; 1117.0bp to feature; MODIFIER	silent_mutation	Average:51.068; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N
vg0913451651	G -> T	LOC_Os09g22240.1	intron_variant ; MODIFIER	silent_mutation	Average:51.068; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913451651	2.49E-06	NA	mr1865	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
vg0913451651	NA	1.66E-07	mr1749_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