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Detailed information for vg1210098198:

Variant ID: vg1210098198 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 10098198
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAGTAGCAAACGGAAAACCACAAACGTGGCTACTCATTTTGATTCTGGAGAGATATAGCTGGTATTGTTCTAGTGACTGCATCCTGGATTGGTTCTGT[G/A]
ATGATGTGTTAGGACTGCATATTGCTATCATTCACAGGAGAAGCTTCCTTCTGATTGCTAGTTGAAGCGGATAATGGTCTTCTGCTTCGTATCGCCCTCC

Reverse complement sequence

GGAGGGCGATACGAAGCAGAAGACCATTATCCGCTTCAACTAGCAATCAGAAGGAAGCTTCTCCTGTGAATGATAGCAATATGCAGTCCTAACACATCAT[C/T]
ACAGAACCAATCCAGGATGCAGTCACTAGAACAATACCAGCTATATCTCTCCAGAATCAAAATGAGTAGCCACGTTTGTGGTTTTCCGTTTGCTACTTAT

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	69.00%	0.10%	12.51%	18.30%	NA
All Indica	2759	60.20%	0.30%	17.72%	21.78%	NA
All Japonica	1512	88.60%	0.00%	3.37%	8.07%	NA
Aus	269	42.40%	0.00%	16.73%	40.89%	NA
Indica I	595	45.90%	0.50%	15.46%	38.15%	NA
Indica II	465	66.70%	0.00%	13.76%	19.57%	NA
Indica III	913	67.60%	0.20%	22.45%	9.75%	NA
Indica Intermediate	786	58.80%	0.30%	16.28%	24.68%	NA
Temperate Japonica	767	89.20%	0.00%	3.26%	7.56%	NA
Tropical Japonica	504	87.50%	0.00%	3.57%	8.93%	NA
Japonica Intermediate	241	88.80%	0.00%	3.32%	7.88%	NA
VI/Aromatic	96	79.20%	0.00%	3.12%	17.71%	NA
Intermediate	90	80.00%	0.00%	3.33%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1210098198	G -> DEL	N	N	silent_mutation	Average:20.002; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N
vg1210098198	G -> A	LOC_Os12g17620.1	upstream_gene_variant ; 4662.0bp to feature; MODIFIER	silent_mutation	Average:20.002; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N
vg1210098198	G -> A	LOC_Os12g17630.1	downstream_gene_variant ; 58.0bp to feature; MODIFIER	silent_mutation	Average:20.002; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N
vg1210098198	G -> A	LOC_Os12g17620-LOC_Os12g17630	intergenic_region ; MODIFIER	silent_mutation	Average:20.002; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1210098198	4.60E-06	3.40E-06	mr1825_2	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