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Detailed information for vg1204346951:

Variant ID: vg1204346951 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4346951
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGCGATGGATGGAACCCAACAGGGTATCTGGATGCGTTGCATTCCAACTTCGGGATCGGCTGAAGTCGCGTTACATCCCCTTCCAATGCCCCTCTTCTC[A/G]
CAGCAAGTGGCGGGCGAGATGGTTCTATCTTCAGATAGAAAACTCGGATCCCGTCCTTGTTGTCCCTAAAGAACAACCAAACAAAATCCCTGAGTGGACC

Reverse complement sequence

GGTCCACTCAGGGATTTTGTTTGGTTGTTCTTTAGGGACAACAAGGACGGGATCCGAGTTTTCTATCTGAAGATAGAACCATCTCGCCCGCCACTTGCTG[T/C]
GAGAAGAGGGGCATTGGAAGGGGATGTAACGCGACTTCAGCCGATCCCGAAGTTGGAATGCAACGCATCCAGATACCCTGTTGGGTTCCATCCATCGCAG

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	54.30%	33.90%	1.93%	9.80%	NA
All Indica	2759	78.50%	20.80%	0.69%	0.04%	NA
All Japonica	1512	9.60%	55.40%	4.63%	30.36%	NA
Aus	269	48.70%	50.90%	0.37%	0.00%	NA
Indica I	595	62.90%	36.30%	0.84%	0.00%	NA
Indica II	465	72.50%	26.90%	0.65%	0.00%	NA
Indica III	913	95.30%	4.10%	0.66%	0.00%	NA
Indica Intermediate	786	74.40%	24.80%	0.64%	0.13%	NA
Temperate Japonica	767	2.50%	80.60%	5.74%	11.21%	NA
Tropical Japonica	504	21.80%	27.40%	2.58%	48.21%	NA
Japonica Intermediate	241	6.60%	34.00%	5.39%	53.94%	NA
VI/Aromatic	96	82.30%	16.70%	1.04%	0.00%	NA
Intermediate	90	52.20%	44.40%	0.00%	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
vg1204346951	A -> DEL	N	N	silent_mutation	Average:22.71; most accessible tissue: Callus, score: 41.426	N	N	N	N
vg1204346951	A -> G	LOC_Os12g08564.1	intron_variant ; MODIFIER	silent_mutation	Average:22.71; most accessible tissue: Callus, score: 41.426	N	N	N	N
vg1204346951	A -> G	LOC_Os12g08564.3	intron_variant ; MODIFIER	silent_mutation	Average:22.71; most accessible tissue: Callus, score: 41.426	N	N	N	N
vg1204346951	A -> G	LOC_Os12g08564.4	intron_variant ; MODIFIER	silent_mutation	Average:22.71; most accessible tissue: Callus, score: 41.426	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204346951	9.62E-06	NA	mr1002	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
vg1204346951	1.22E-06	4.29E-06	mr1269	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