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Detailed information for vg1206630456:

Variant ID: vg1206630456 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6630456
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTCTGTCGATGTTTTGCCACTGCAACCCATTGGTGGGGTGTCTCAGCATCCTGTCTTGTTGATGTTTTTCTGCGTGCCAACGCATTATTCTAGCATGCG[C/T]
TTTCTTCCTGAACAAACGCCTCAGCCATGGTATTATAGGGAAATAACACATCAACTTAGTTGGAACTCTCTTTTTTGAAGGTTGTCCGTCAACATCACCT

Reverse complement sequence

AGGTGATGTTGACGGACAACCTTCAAAAAAGAGAGTTCCAACTAAGTTGATGTGTTATTTCCCTATAATACCATGGCTGAGGCGTTTGTTCAGGAAGAAA[G/A]
CGCATGCTAGAATAATGCGTTGGCACGCAGAAAAACATCAACAAGACAGGATGCTGAGACACCCCACCAATGGGTTGCAGTGGCAAAACATCGACAGAAC

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	29.30%	14.50%	5.10%	51.08%	NA
All Indica	2759	4.40%	9.80%	8.30%	77.49%	NA
All Japonica	1512	75.50%	21.00%	0.07%	3.37%	NA
Aus	269	28.60%	22.30%	1.86%	47.21%	NA
Indica I	595	4.70%	15.50%	10.25%	69.58%	NA
Indica II	465	3.70%	11.60%	6.88%	77.85%	NA
Indica III	913	2.30%	4.70%	8.65%	84.34%	NA
Indica Intermediate	786	7.00%	10.40%	7.25%	75.32%	NA
Temperate Japonica	767	67.70%	27.80%	0.13%	4.43%	NA
Tropical Japonica	504	93.50%	4.20%	0.00%	2.38%	NA
Japonica Intermediate	241	63.10%	34.90%	0.00%	2.07%	NA
VI/Aromatic	96	3.10%	20.80%	6.25%	69.79%	NA
Intermediate	90	47.80%	17.80%	0.00%	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
vg1206630456	C -> DEL	N	N	silent_mutation	Average:17.823; most accessible tissue: Callus, score: 35.346	N	N	N	N
vg1206630456	C -> T	LOC_Os12g12100.1	upstream_gene_variant ; 892.0bp to feature; MODIFIER	silent_mutation	Average:17.823; most accessible tissue: Callus, score: 35.346	N	N	N	N
vg1206630456	C -> T	LOC_Os12g12090.1	downstream_gene_variant ; 4414.0bp to feature; MODIFIER	silent_mutation	Average:17.823; most accessible tissue: Callus, score: 35.346	N	N	N	N
vg1206630456	C -> T	LOC_Os12g12100-LOC_Os12g12110	intergenic_region ; MODIFIER	silent_mutation	Average:17.823; most accessible tissue: Callus, score: 35.346	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206630456	1.13E-06	NA	mr1149	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