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Detailed information for vg1220360803:

Variant ID: vg1220360803 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20360803
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: 53. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGGAAGCAGTTATCTACCGAACTGGACTTGGGCCGGGGTAAACGGCCTCTGCCAGGGTTTGGCCGAACTCAGGGGTTCGGCTGAACCCGGGACGGCTC[C/T]
GTTCGCTCCGGTTTTCATCCTGGACACTCATTTTGGGCCCCCCCCAATTCATTGCTATGAATGTTTGGCCCATTTGGACGTGTTTAATTGGGTTTATGGG

Reverse complement sequence

CCCATAAACCCAATTAAACACGTCCAAATGGGCCAAACATTCATAGCAATGAATTGGGGGGGGCCCAAAATGAGTGTCCAGGATGAAAACCGGAGCGAAC[G/A]
GAGCCGTCCCGGGTTCAGCCGAACCCCTGAGTTCGGCCAAACCCTGGCAGAGGCCGTTTACCCCGGCCCAAGTCCAGTTCGGTAGATAACTGCTTCCCAA

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	39.70%	3.80%	7.64%	48.84%	NA
All Indica	2759	26.10%	3.70%	11.56%	58.61%	NA
All Japonica	1512	69.00%	4.30%	1.46%	25.20%	NA
Aus	269	19.70%	0.40%	2.60%	77.32%	NA
Indica I	595	45.20%	7.90%	15.80%	31.09%	NA
Indica II	465	23.40%	1.30%	9.46%	65.81%	NA
Indica III	913	16.20%	2.20%	10.41%	71.19%	NA
Indica Intermediate	786	24.70%	3.80%	10.94%	60.56%	NA
Temperate Japonica	767	94.80%	0.00%	0.00%	5.22%	NA
Tropical Japonica	504	31.20%	12.30%	3.97%	52.58%	NA
Japonica Intermediate	241	66.40%	1.20%	0.83%	31.54%	NA
VI/Aromatic	96	11.50%	7.30%	6.25%	75.00%	NA
Intermediate	90	53.30%	5.60%	7.78%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220360803	C -> DEL	N	N	silent_mutation	Average:18.857; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg1220360803	C -> T	LOC_Os12g33750.1	upstream_gene_variant ; 4162.0bp to feature; MODIFIER	silent_mutation	Average:18.857; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg1220360803	C -> T	LOC_Os12g33730.1	downstream_gene_variant ; 3791.0bp to feature; MODIFIER	silent_mutation	Average:18.857; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg1220360803	C -> T	LOC_Os12g33740.1	downstream_gene_variant ; 1765.0bp to feature; MODIFIER	silent_mutation	Average:18.857; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg1220360803	C -> T	LOC_Os12g33740-LOC_Os12g33750	intergenic_region ; MODIFIER	silent_mutation	Average:18.857; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220360803	NA	1.54E-06	mr1817	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