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Detailed information for vg1212722845:

Variant ID: vg1212722845 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 12722845
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.35, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTGGTTATATTTATAGAGGGGGTGATTATGATCCAGGAATGGTGCACTATGGTGAGTTGTGTTGTGCAGGGGGTACTGTCACAGCCTCTATTCGGGTA[C/T]
TTTCCAGTATCGCGACGCATGGTAGACATGATGTTGAGGCTGTGTCTTGTGTGTACAGTGGTACACCTCTGGCCAGAGTAAAACTATTCGAATAGCCGTG

Reverse complement sequence

CACGGCTATTCGAATAGTTTTACTCTGGCCAGAGGTGTACCACTGTACACACAAGACACAGCCTCAACATCATGTCTACCATGCGTCGCGATACTGGAAA[G/A]
TACCCGAATAGAGGCTGTGACAGTACCCCCTGCACAACACAACTCACCATAGTGCACCATTCCTGGATCATAATCACCCCCTCTATAAATATAACCAGAG

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	71.40%	28.50%	0.11%	0.02%	NA
All Indica	2759	76.70%	23.20%	0.11%	0.00%	NA
All Japonica	1512	55.60%	44.30%	0.13%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	97.10%	2.90%	0.00%	0.00%	NA
Indica II	465	61.50%	38.30%	0.22%	0.00%	NA
Indica III	913	74.90%	25.00%	0.11%	0.00%	NA
Indica Intermediate	786	72.10%	27.70%	0.13%	0.00%	NA
Temperate Japonica	767	22.70%	77.30%	0.00%	0.00%	NA
Tropical Japonica	504	95.80%	3.80%	0.40%	0.00%	NA
Japonica Intermediate	241	75.90%	24.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	64.40%	34.40%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1212722845	C -> DEL	N	N	silent_mutation	Average:54.28; most accessible tissue: Zhenshan97 flag leaf, score: 76.642	N	N	N	N
vg1212722845	C -> T	LOC_Os12g22530.1	downstream_gene_variant ; 4391.0bp to feature; MODIFIER	silent_mutation	Average:54.28; most accessible tissue: Zhenshan97 flag leaf, score: 76.642	N	N	N	N
vg1212722845	C -> T	LOC_Os12g22540.1	intron_variant ; MODIFIER	silent_mutation	Average:54.28; most accessible tissue: Zhenshan97 flag leaf, score: 76.642	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1212722845	NA	1.19E-06	mr1425	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
vg1212722845	NA	5.32E-08	mr1942	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
vg1212722845	NA	4.56E-08	mr1338_2	Jap_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
vg1212722845	NA	4.51E-07	mr1425_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
vg1212722845	NA	4.67E-13	mr1942_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