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Detailed information for vg1214644369:

Variant ID: vg1214644369 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14644369
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GCACTCAAGGTAGACATGATACCAGCAGATTTAAACACAGTTTTGTTAGTATCAGGTTTAACCAAAATCTCACCACTTCTAGCACCAACACCTAACACAA[C/T]
AAGAGGATGTCTAGAATTATGAGCATAAGGGTTAAAACCTAAACCACGATTATGTGTGCTAACCTTTGATTGATCCAAAATTATGTTGAGGTTCTTCTTA

Reverse complement sequence

TAAGAAGAACCTCAACATAATTTTGGATCAATCAAAGGTTAGCACACATAATCGTGGTTTAGGTTTTAACCCTTATGCTCATAATTCTAGACATCCTCTT[G/A]
TTGTGTTAGGTGTTGGTGCTAGAAGTGGTGAGATTTTGGTTAAACCTGATACTAACAAAACTGTGTTTAAATCTGCTGGTATCATGTCTACCTTGAGTGC

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	68.10%	15.60%	10.07%	6.22%	NA
All Indica	2759	56.60%	16.20%	16.82%	10.40%	NA
All Japonica	1512	99.30%	0.50%	0.13%	0.13%	NA
Aus	269	25.30%	74.00%	0.74%	0.00%	NA
Indica I	595	58.70%	22.20%	12.10%	7.06%	NA
Indica II	465	68.60%	3.20%	18.28%	9.89%	NA
Indica III	913	48.70%	16.20%	22.12%	12.92%	NA
Indica Intermediate	786	57.10%	19.20%	13.36%	10.31%	NA
Temperate Japonica	767	99.30%	0.30%	0.26%	0.13%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	1.70%	0.00%	0.41%	NA
VI/Aromatic	96	19.80%	70.80%	6.25%	3.12%	NA
Intermediate	90	76.70%	18.90%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214644369	C -> DEL	N	N	silent_mutation	Average:16.792; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg1214644369	C -> T	LOC_Os12g25390.1	downstream_gene_variant ; 3994.0bp to feature; MODIFIER	silent_mutation	Average:16.792; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg1214644369	C -> T	LOC_Os12g25380.1	intron_variant ; MODIFIER	silent_mutation	Average:16.792; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214644369	3.82E-06	NA	mr1333	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
vg1214644369	NA	4.25E-06	mr1336	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
vg1214644369	NA	1.60E-06	mr1803	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