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Detailed information for vg1222304933:

Variant ID: vg1222304933 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22304933
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

GAGCTAAAACATGGACGATCATGCACTCCCTTCGAGCCAGCAGCACCTGCAACCTTCAGAGGGCTCAGATGCCATTCATCAAATAACGGTAAGAAACGCA[T/C]
TGTTGCTCTTCCAATTTTGTTTCACCAATTCTTTCCTGCAAAATGAAACAGATGAAAGAAATGGCTATTGTTTGCTCCATCACGAGAGATAAAAAGGGAA

Reverse complement sequence

TTCCCTTTTTATCTCTCGTGATGGAGCAAACAATAGCCATTTCTTTCATCTGTTTCATTTTGCAGGAAAGAATTGGTGAAACAAAATTGGAAGAGCAACA[A/G]
TGCGTTTCTTACCGTTATTTGATGAATGGCATCTGAGCCCTCTGAAGGTTGCAGGTGCTGCTGGCTCGAAGGGAGTGCATGATCGTCCATGTTTTAGCTC

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	86.10%	12.40%	1.52%	0.00%	NA
All Indica	2759	83.60%	14.00%	2.43%	0.00%	NA
All Japonica	1512	99.70%	0.10%	0.20%	0.00%	NA
Aus	269	29.70%	69.90%	0.37%	0.00%	NA
Indica I	595	88.60%	11.30%	0.17%	0.00%	NA
Indica II	465	90.50%	3.00%	6.45%	0.00%	NA
Indica III	913	81.10%	18.70%	0.22%	0.00%	NA
Indica Intermediate	786	78.80%	16.90%	4.33%	0.00%	NA
Temperate Japonica	767	99.60%	0.00%	0.39%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	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
vg1222304933	T -> C	LOC_Os12g36440.1	upstream_gene_variant ; 3048.0bp to feature; MODIFIER	silent_mutation	Average:43.497; most accessible tissue: Callus, score: 72.188	N	N	N	N
vg1222304933	T -> C	LOC_Os12g36450.1	upstream_gene_variant ; 165.0bp to feature; MODIFIER	silent_mutation	Average:43.497; most accessible tissue: Callus, score: 72.188	N	N	N	N
vg1222304933	T -> C	LOC_Os12g36440-LOC_Os12g36450	intergenic_region ; MODIFIER	silent_mutation	Average:43.497; most accessible tissue: Callus, score: 72.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222304933	NA	6.14E-06	mr1176	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
vg1222304933	NA	7.02E-06	mr1544	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
vg1222304933	NA	4.34E-06	mr1631	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
vg1222304933	2.83E-06	5.61E-08	mr1716	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
vg1222304933	NA	2.60E-06	mr1931	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
vg1222304933	NA	7.66E-07	mr1952	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
vg1222304933	NA	3.34E-06	mr1574_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