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Detailed information for vg1221860511:

Variant ID: vg1221860511 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21860511
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.81, C: 0.19, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGAGTGCAAAAAATAAGAAGTGTGAGAAGATGTATAGAAAATAGGAGTTTATCATTGAATCTCTTAAATCTGAAATTGATAGGTTAAAATCTCTTATT[T/C]
CTAATGATGATGATTGTGAAAATTGTGAGGTTTTAATGAATGAGATTTCAAAAATTAGAGTTGTTAATGCTGCACATGATTTGAAAAATAGATCTTCTCT

Reverse complement sequence

AGAGAAGATCTATTTTTCAAATCATGTGCAGCATTAACAACTCTAATTTTTGAAATCTCATTCATTAAAACCTCACAATTTTCACAATCATCATCATTAG[A/G]
AATAAGAGATTTTAACCTATCAATTTCAGATTTAAGAGATTCAATGATAAACTCCTATTTTCTATACATCTTCTCACACTTCTTATTTTTTGCACTCAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.20%	0.50%	23.99%	35.29%	NA
All Indica	2759	11.00%	0.70%	29.14%	59.15%	NA
All Japonica	1512	94.80%	0.10%	4.76%	0.33%	NA
Aus	269	15.60%	0.40%	78.81%	5.20%	NA
Indica I	595	22.20%	0.20%	23.03%	54.62%	NA
Indica II	465	10.30%	0.60%	33.55%	55.48%	NA
Indica III	913	4.50%	1.50%	29.13%	64.84%	NA
Indica Intermediate	786	10.40%	0.30%	31.17%	58.14%	NA
Temperate Japonica	767	96.20%	0.10%	3.26%	0.39%	NA
Tropical Japonica	504	91.30%	0.20%	8.33%	0.20%	NA
Japonica Intermediate	241	97.50%	0.00%	2.07%	0.41%	NA
VI/Aromatic	96	61.50%	0.00%	33.33%	5.21%	NA
Intermediate	90	71.10%	0.00%	15.56%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221860511	T -> C	LOC_Os12g35870.1	upstream_gene_variant ; 3123.0bp to feature; MODIFIER	silent_mutation	Average:9.638; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg1221860511	T -> C	LOC_Os12g35880.1	intron_variant ; MODIFIER	silent_mutation	Average:9.638; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg1221860511	T -> DEL	N	N	silent_mutation	Average:9.638; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221860511	7.43E-06	NA	mr1841	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
vg1221860511	2.88E-06	2.88E-06	mr1487_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