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Detailed information for vg1213198370:

Variant ID: vg1213198370 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13198370
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

GGGATCTTTAGTCTCGGTTGCTAACACCAACCGGGACTAAAAAGAGGGAAGCGGCAGTGAGATGGTCCCCTTTTCTTTTTTTTCTTTTTTATTTTCTCCC[G/A]
AATCGAGTGGGATATATATCCCAAATCAAACCCAAATCCCCAAATCAAAGTAACATCTCAAATCTACATCACAAATCTTAAAGTTACTTATACACACAAA

Reverse complement sequence

TTTGTGTGTATAAGTAACTTTAAGATTTGTGATGTAGATTTGAGATGTTACTTTGATTTGGGGATTTGGGTTTGATTTGGGATATATATCCCACTCGATT[C/T]
GGGAGAAAATAAAAAAGAAAAAAAAGAAAAGGGGACCATCTCACTGCCGCTTCCCTCTTTTTAGTCCCGGTTGGTGTTAGCAACCGAGACTAAAGATCCC

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	72.60%	3.10%	5.10%	19.17%	NA
All Indica	2759	55.60%	5.30%	8.12%	31.06%	NA
All Japonica	1512	97.00%	0.10%	0.99%	1.98%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	39.80%	2.70%	6.55%	50.92%	NA
Indica II	465	60.20%	0.40%	6.88%	32.47%	NA
Indica III	913	58.10%	8.30%	11.28%	22.34%	NA
Indica Intermediate	786	61.80%	6.50%	6.36%	25.32%	NA
Temperate Japonica	767	96.90%	0.10%	0.39%	2.61%	NA
Tropical Japonica	504	96.80%	0.00%	1.59%	1.59%	NA
Japonica Intermediate	241	97.50%	0.00%	1.66%	0.83%	NA
VI/Aromatic	96	89.60%	0.00%	2.08%	8.33%	NA
Intermediate	90	87.80%	0.00%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213198370	G -> DEL	N	N	silent_mutation	Average:35.491; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1213198370	G -> A	LOC_Os12g23300.1	upstream_gene_variant ; 1185.0bp to feature; MODIFIER	silent_mutation	Average:35.491; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1213198370	G -> A	LOC_Os12g23310.1	upstream_gene_variant ; 1408.0bp to feature; MODIFIER	silent_mutation	Average:35.491; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1213198370	G -> A	LOC_Os12g23320.1	downstream_gene_variant ; 2447.0bp to feature; MODIFIER	silent_mutation	Average:35.491; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1213198370	G -> A	LOC_Os12g23300-LOC_Os12g23310	intergenic_region ; MODIFIER	silent_mutation	Average:35.491; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213198370	4.92E-06	NA	mr1133_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
vg1213198370	9.20E-06	9.20E-06	mr1171_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
vg1213198370	NA	1.29E-06	mr1272_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
vg1213198370	NA	9.93E-08	mr1308_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