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Detailed information for vg1212917013:

Variant ID: vg1212917013 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 12917013
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AACCCGTTTGAGGTGAGGTAACCTCACCTGTGACGGGATCTATTTTTAACCCGTCACAGGTGACTAGTTACCTGTGACGGGTAACAGCCGGATGCCTCAC[C/T]
GATGACGGCATCCCGTATGACCCGTCAGAGGTGACGGTCATCAGTGACCATTTCGATTGCCCGTCACAGGTATCTCGTCAGAGATGTGAGGATCTGGTGT

Reverse complement sequence

ACACCAGATCCTCACATCTCTGACGAGATACCTGTGACGGGCAATCGAAATGGTCACTGATGACCGTCACCTCTGACGGGTCATACGGGATGCCGTCATC[G/A]
GTGAGGCATCCGGCTGTTACCCGTCACAGGTAACTAGTCACCTGTGACGGGTTAAAAATAGATCCCGTCACAGGTGAGGTTACCTCACCTCAAACGGGTT

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	89.70%	9.70%	0.13%	0.44%	NA
All Indica	2759	82.70%	16.30%	0.18%	0.76%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	55.50%	44.20%	0.17%	0.17%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	91.90%	6.70%	0.22%	1.20%	NA
Indica Intermediate	786	85.40%	13.20%	0.25%	1.15%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1212917013	C -> DEL	N	N	silent_mutation	Average:67.692; most accessible tissue: Minghui63 panicle, score: 86.012	N	N	N	N
vg1212917013	C -> T	LOC_Os12g22880.1	downstream_gene_variant ; 3838.0bp to feature; MODIFIER	silent_mutation	Average:67.692; most accessible tissue: Minghui63 panicle, score: 86.012	N	N	N	N
vg1212917013	C -> T	LOC_Os12g22880-LOC_Os12g22890	intergenic_region ; MODIFIER	silent_mutation	Average:67.692; most accessible tissue: Minghui63 panicle, score: 86.012	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1212917013	NA	6.84E-06	mr1164_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
vg1212917013	NA	1.18E-06	mr1170_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
vg1212917013	NA	3.54E-07	mr1308_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
vg1212917013	NA	1.94E-06	mr1469_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
vg1212917013	NA	5.03E-06	mr1469_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
vg1212917013	NA	6.14E-06	mr1745_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