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Detailed information for vg1222419871:

Variant ID: vg1222419871 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22419871
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.64, C: 0.36, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTCATCACATCAAAACTTTCCTACACACACAAATTTCCAACTTTTCCGTCACATCATTCCAATTTTAACCAAATTTCTAATTTTGGCGTTGATTTGA[T/C]
ATGATTTGACAATGTGATGCTACCGTAAATATTTGCTAATGACAGATTAATTAGGCTTAATAGATTCGTCTCGCAGTTTATATGCGGAATTTATAATTTG

Reverse complement sequence

CAAATTATAAATTCCGCATATAAACTGCGAGACGAATCTATTAAGCCTAATTAATCTGTCATTAGCAAATATTTACGGTAGCATCACATTGTCAAATCAT[A/G]
TCAAATCAACGCCAAAATTAGAAATTTGGTTAAAATTGGAATGATGTGACGGAAAAGTTGGAAATTTGTGTGTGTAGGAAAGTTTTGATGTGATGAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.30%	24.40%	0.36%	43.91%	NA
All Indica	2759	35.70%	2.80%	0.51%	61.00%	NA
All Japonica	1512	19.00%	67.80%	0.07%	13.16%	NA
Aus	269	34.90%	1.10%	0.37%	63.57%	NA
Indica I	595	38.20%	1.80%	0.34%	59.66%	NA
Indica II	465	17.20%	3.70%	0.22%	78.92%	NA
Indica III	913	43.30%	1.90%	0.77%	54.11%	NA
Indica Intermediate	786	36.10%	3.90%	0.51%	59.41%	NA
Temperate Japonica	767	13.80%	77.60%	0.00%	8.60%	NA
Tropical Japonica	504	13.10%	65.30%	0.20%	21.43%	NA
Japonica Intermediate	241	47.70%	41.90%	0.00%	10.37%	NA
VI/Aromatic	96	87.50%	7.30%	0.00%	5.21%	NA
Intermediate	90	33.30%	46.70%	1.11%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222419871	T -> C	LOC_Os12g36600.1	downstream_gene_variant ; 4255.0bp to feature; MODIFIER	silent_mutation	Average:6.272; most accessible tissue: Callus, score: 19.452	N	N	N	N
vg1222419871	T -> C	LOC_Os12g36610.1	downstream_gene_variant ; 606.0bp to feature; MODIFIER	silent_mutation	Average:6.272; most accessible tissue: Callus, score: 19.452	N	N	N	N
vg1222419871	T -> C	LOC_Os12g36620.1	intron_variant ; MODIFIER	silent_mutation	Average:6.272; most accessible tissue: Callus, score: 19.452	N	N	N	N
vg1222419871	T -> DEL	N	N	silent_mutation	Average:6.272; most accessible tissue: Callus, score: 19.452	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222419871	NA	3.02E-06	mr1227_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
vg1222419871	NA	1.18E-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