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Detailed information for vg1222716971:

Variant ID: vg1222716971 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22716971
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCATAGAATAGTTTTGGTTGCTATGTCAATTTTCTAACCGCTTATCGGTTGTAGAGCAGGGTGTGTTCGTTGGAGCTGGTTCCCAACCAGCACAGTACG[C/T]
ACGGAAAACGGAGCGATCTATTAGCGCGTGTATTAGCTAATTTTTTTTTAAAAATGGAATAATATGATTTTTTTAAACAACTTTCGTATAGATTTTTTTT

Reverse complement sequence

AAAAAAAATCTATACGAAAGTTGTTTAAAAAAATCATATTATTCCATTTTTAAAAAAAAATTAGCTAATACACGCGCTAATAGATCGCTCCGTTTTCCGT[G/A]
CGTACTGTGCTGGTTGGGAACCAGCTCCAACGAACACACCCTGCTCTACAACCGATAAGCGGTTAGAAAATTGACATAGCAACCAAAACTATTCTATGAG

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	92.10%	5.10%	2.81%	0.00%	NA
All Indica	2759	98.40%	0.40%	1.27%	0.00%	NA
All Japonica	1512	79.00%	14.80%	6.22%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	94.80%	0.20%	5.04%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	99.20%	0.70%	0.11%	0.00%	NA
Indica Intermediate	786	99.50%	0.10%	0.38%	0.00%	NA
Temperate Japonica	767	91.00%	1.40%	7.56%	0.00%	NA
Tropical Japonica	504	56.00%	39.90%	4.17%	0.00%	NA
Japonica Intermediate	241	88.80%	5.00%	6.22%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	6.70%	3.33%	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
vg1222716971	C -> T	LOC_Os12g37060.1	upstream_gene_variant ; 3622.0bp to feature; MODIFIER	silent_mutation	Average:41.642; most accessible tissue: Callus, score: 75.958	N	N	N	N
vg1222716971	C -> T	LOC_Os12g37080.1	downstream_gene_variant ; 2471.0bp to feature; MODIFIER	silent_mutation	Average:41.642; most accessible tissue: Callus, score: 75.958	N	N	N	N
vg1222716971	C -> T	LOC_Os12g37090.1	downstream_gene_variant ; 4896.0bp to feature; MODIFIER	silent_mutation	Average:41.642; most accessible tissue: Callus, score: 75.958	N	N	N	N
vg1222716971	C -> T	LOC_Os12g37070.1	intron_variant ; MODIFIER	silent_mutation	Average:41.642; most accessible tissue: Callus, score: 75.958	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222716971	1.48E-06	1.48E-06	mr1068	Jap_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
vg1222716971	NA	6.28E-07	mr1090	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