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Detailed information for vg1214644112:

Variant ID: vg1214644112 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14644112
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, T: 0.23, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GGGACCCACTGCGGTCTGACCGGTTTCCTCGAGGGAAAACCAGATTTTTGCCACTTTGATTTTGCAAAAGCAATCTCTCTCTCCTTTTTCTGTTTATGAG[T/C]
TAATCTGAAACAAAAACCAATAATATGTCCATCTTTTCCAAAAAAGAACAAGTATATTTTTCACGATGATTAGACACATTGGTAGTATTAGAAGATTTAG

Reverse complement sequence

CTAAATCTTCTAATACTACCAATGTGTCTAATCATCGTGAAAAATATACTTGTTCTTTTTTGGAAAAGATGGACATATTATTGGTTTTTGTTTCAGATTA[A/G]
CTCATAAACAGAAAAAGGAGAGAGAGATTGCTTTTGCAAAATCAAAGTGGCAAAAATCTGGTTTTCCCTCGAGGAAACCGGTCAGACCGCAGTGGGTCCC

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	18.00%	10.60%	27.25%	44.14%	NA
All Indica	2759	15.50%	1.00%	20.95%	62.52%	NA
All Japonica	1512	27.20%	29.90%	22.62%	20.24%	NA
Aus	269	0.70%	0.40%	93.31%	5.58%	NA
Indica I	595	47.10%	0.30%	17.82%	34.79%	NA
Indica II	465	6.20%	1.10%	17.63%	75.05%	NA
Indica III	913	1.50%	0.30%	23.00%	75.14%	NA
Indica Intermediate	786	13.40%	2.30%	22.90%	61.45%	NA
Temperate Japonica	767	30.60%	53.20%	6.13%	10.04%	NA
Tropical Japonica	504	17.90%	1.60%	48.02%	32.54%	NA
Japonica Intermediate	241	36.10%	14.90%	21.99%	26.97%	NA
VI/Aromatic	96	0.00%	1.00%	89.58%	9.38%	NA
Intermediate	90	8.90%	22.20%	34.44%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214644112	T -> C	LOC_Os12g25390.1	downstream_gene_variant ; 4251.0bp to feature; MODIFIER	silent_mutation	Average:29.678; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg1214644112	T -> C	LOC_Os12g25380.1	intron_variant ; MODIFIER	silent_mutation	Average:29.678; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N
vg1214644112	T -> DEL	N	N	silent_mutation	Average:29.678; most accessible tissue: Minghui63 young leaf, score: 49.581	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214644112	4.80E-09	NA	mr1310_2	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
vg1214644112	NA	2.12E-07	mr1959_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