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Detailed information for vg0322301990:

Variant ID: vg0322301990 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22301990
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCACCAAAGTTACAACGTCCATAAGTGTCGCCATTGTTAGCCTCGAATAGGCTAGACTTTTGCCATAAACCTTCTACCCTCTCATGTCAAAGCACCTT[T/C]
AGCGTGGAACCATCGTGCCAACGCCACGCTGCCAACTGACCATTAGGTAGGGCTTGACATTTGCAAGCCACCCTACGCCAAACTCACTTCCCACGTTGTT

Reverse complement sequence

AACAACGTGGGAAGTGAGTTTGGCGTAGGGTGGCTTGCAAATGTCAAGCCCTACCTAATGGTCAGTTGGCAGCGTGGCGTTGGCACGATGGTTCCACGCT[A/G]
AAGGTGCTTTGACATGAGAGGGTAGAAGGTTTATGGCAAAAGTCTAGCCTATTCGAGGCTAACAATGGCGACACTTATGGACGTTGTAACTTTGGTGAGG

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	82.30%	17.40%	0.06%	0.30%	NA
All Indica	2759	70.40%	29.10%	0.07%	0.47%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	87.40%	12.40%	0.00%	0.17%	NA
Indica II	465	94.20%	5.40%	0.00%	0.43%	NA
Indica III	913	53.60%	45.60%	0.22%	0.66%	NA
Indica Intermediate	786	63.00%	36.50%	0.00%	0.51%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	11.10%	1.11%	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
vg0322301990	T -> C	LOC_Os03g40130.1	upstream_gene_variant ; 1840.0bp to feature; MODIFIER	silent_mutation	Average:63.143; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N
vg0322301990	T -> C	LOC_Os03g40130-LOC_Os03g40160	intergenic_region ; MODIFIER	silent_mutation	Average:63.143; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N
vg0322301990	T -> DEL	N	N	silent_mutation	Average:63.143; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322301990	NA	6.37E-07	mr1221	Ind_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
vg0322301990	NA	3.61E-06	mr1422	Ind_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
vg0322301990	1.69E-06	1.69E-06	mr1884	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