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Detailed information for vg1121387639:

Variant ID: vg1121387639 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21387639
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

GTGAGAGATGGCTACGTACTGGTTCGAGGACCAGCGAATGAACGTTTAGAATTATCTCTCGAACACCAATGGGGGTGCTAGAGTTGGTTTATTACATGTG[C/T]
GTCTCATGTGGCCAACATGACTCACGCACCCAACTTATAGCATATCCGGATGTCCGTTCGCAATCATGTCGGGAGATCAAGCCGACGACGTTCGCGAGAA

Reverse complement sequence

TTCTCGCGAACGTCGTCGGCTTGATCTCCCGACATGATTGCGAACGGACATCCGGATATGCTATAAGTTGGGTGCGTGAGTCATGTTGGCCACATGAGAC[G/A]
CACATGTAATAAACCAACTCTAGCACCCCCATTGGTGTTCGAGAGATAATTCTAAACGTTCATTCGCTGGTCCTCGAACCAGTACGTAGCCATCTCTCAC

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	96.40%	0.40%	2.41%	0.83%	NA
All Indica	2759	95.50%	0.60%	3.23%	0.69%	NA
All Japonica	1512	97.40%	0.10%	1.39%	1.12%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	94.50%	0.30%	4.20%	1.01%	NA
Indica II	465	93.10%	1.10%	4.95%	0.86%	NA
Indica III	913	97.70%	0.30%	1.42%	0.55%	NA
Indica Intermediate	786	95.00%	0.90%	3.56%	0.51%	NA
Temperate Japonica	767	97.10%	0.00%	1.30%	1.56%	NA
Tropical Japonica	504	96.80%	0.20%	1.98%	0.99%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	0.00%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121387639	C -> T	LOC_Os11g36310.1	upstream_gene_variant ; 3843.0bp to feature; MODIFIER	silent_mutation	Average:44.449; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg1121387639	C -> T	LOC_Os11g36320.1	intron_variant ; MODIFIER	silent_mutation	Average:44.449; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg1121387639	C -> DEL	N	N	silent_mutation	Average:44.449; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121387639	NA	6.85E-07	mr1126_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
vg1121387639	2.16E-06	2.15E-06	mr1126_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