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Detailed information for vg1211620649:

Variant ID: vg1211620649 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 11620649
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GACTCAACGTCTTCTCACCGTGTTAGAGAAGCATCGTTCTGTTCTTGGCTACTCGCTTCAGGACCTTAGGGGGATTAATCCCGCGCTTTGCACCCATCGT[G/A]
TTCCTATTGACCCCGAGGGTACTCCCTCTATGGAACCTCAACGACGGCTCAATAATGCAATGCGATAGGTTGTAAAGACAGAAGTCTTGAAACTCCTGCA

Reverse complement sequence

TGCAGGAGTTTCAAGACTTCTGTCTTTACAACCTATCGCATTGCATTATTGAGCCGTCGTTGAGGTTCCATAGAGGGAGTACCCTCGGGGTCAATAGGAA[C/T]
ACGATGGGTGCAAAGCGCGGGATTAATCCCCCTAAGGTCCTGAAGCGAGTAGCCAAGAACAGAACGATGCTTCTCTAACACGGTGAGAAGACGTTGAGTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.10%	1.40%	10.43%	15.09%	NA
All Indica	2759	78.10%	1.10%	16.53%	4.31%	NA
All Japonica	1512	60.60%	2.50%	1.98%	34.85%	NA
Aus	269	82.20%	0.00%	0.37%	17.47%	NA
Indica I	595	98.20%	0.00%	1.68%	0.17%	NA
Indica II	465	53.10%	1.90%	31.18%	13.76%	NA
Indica III	913	78.40%	1.60%	16.87%	3.07%	NA
Indica Intermediate	786	77.40%	0.60%	18.70%	3.31%	NA
Temperate Japonica	767	85.90%	4.00%	1.43%	8.60%	NA
Tropical Japonica	504	22.40%	0.20%	1.59%	75.79%	NA
Japonica Intermediate	241	60.20%	2.50%	4.56%	32.78%	NA
VI/Aromatic	96	86.50%	0.00%	1.04%	12.50%	NA
Intermediate	90	85.60%	0.00%	5.56%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1211620649	G -> DEL	N	N	silent_mutation	Average:31.64; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	N	N	N	N
vg1211620649	G -> A	LOC_Os12g19930.1	upstream_gene_variant ; 3479.0bp to feature; MODIFIER	silent_mutation	Average:31.64; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	N	N	N	N
vg1211620649	G -> A	LOC_Os12g19950.1	upstream_gene_variant ; 3171.0bp to feature; MODIFIER	silent_mutation	Average:31.64; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	N	N	N	N
vg1211620649	G -> A	LOC_Os12g19960.1	upstream_gene_variant ; 4518.0bp to feature; MODIFIER	silent_mutation	Average:31.64; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	N	N	N	N
vg1211620649	G -> A	LOC_Os12g19940.1	intron_variant ; MODIFIER	silent_mutation	Average:31.64; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1211620649	1.04E-06	4.96E-06	mr1257	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