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Detailed information for vg0906612050:

Variant ID: vg0906612050 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6612050
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

TACATATTCGTAAAATTTGACGAAGAGAAAGACATGAAAACATAAAGGAATGGTGCGATGCATGGTACTCACAGCACGAGCGAAGTCCTGGTCGCGGTGC[C/T,A]
TGGCGTAGAGGTCTCTAGTGCTCGCAACGTGGGGCTGCTTCTCCAAGGACTTCGCGAAGGTGACCCTAGTATGGGTGCATGGCTGGTACTAGCATAGGTA

Reverse complement sequence

TACCTATGCTAGTACCAGCCATGCACCCATACTAGGGTCACCTTCGCGAAGTCCTTGGAGAAGCAGCCCCACGTTGCGAGCACTAGAGACCTCTACGCCA[G/A,T]
GCACCGCGACCAGGACTTCGCTCGTGCTGTGAGTACCATGCATCGCACCATTCCTTTATGTTTTCATGTCTTTCTCTTCGTCAAATTTTACGAATATGTA

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	81.90%	13.60%	2.86%	1.59%	A: 0.06%
All Indica	2759	69.50%	22.90%	4.78%	2.72%	A: 0.11%
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	59.80%	29.90%	6.72%	3.53%	NA
Indica II	465	72.70%	17.00%	5.38%	4.95%	NA
Indica III	913	70.30%	23.30%	3.94%	2.19%	A: 0.22%
Indica Intermediate	786	73.90%	20.60%	3.94%	1.40%	A: 0.13%
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	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	88.90%	8.90%	2.22%	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
vg0906612050	C -> DEL	N	N	silent_mutation	Average:37.874; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N
vg0906612050	C -> T	LOC_Os09g11810.1	upstream_gene_variant ; 1918.0bp to feature; MODIFIER	silent_mutation	Average:37.874; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N
vg0906612050	C -> T	LOC_Os09g11820.1	intron_variant ; MODIFIER	silent_mutation	Average:37.874; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N
vg0906612050	C -> A	LOC_Os09g11810.1	upstream_gene_variant ; 1918.0bp to feature; MODIFIER	silent_mutation	Average:37.874; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N
vg0906612050	C -> A	LOC_Os09g11820.1	intron_variant ; MODIFIER	silent_mutation	Average:37.874; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906612050	1.45E-06	3.59E-07	mr1478_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