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Detailed information for vg0324328837:

Variant ID: vg0324328837 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24328837
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: 97. )

Flanking Sequence (100 bp) in Reference Genome:

CAACAAGAGTTGTACATGGAACGACAAGGACTACTCGGATTGTATCCATATTGGCTTCCCTAGTTCTACTTGGACAAGGGGACACCTATGGGTATAAATA[C/T]
AAGGCCCCCTAAGAGGAGAGGGAACAATCAACACATTCCCACCATAGAAGATACGGAACAATAGATCAAGACAGAAGATTAACATAGAAGCCAATATACG

Reverse complement sequence

CGTATATTGGCTTCTATGTTAATCTTCTGTCTTGATCTATTGTTCCGTATCTTCTATGGTGGGAATGTGTTGATTGTTCCCTCTCCTCTTAGGGGGCCTT[G/A]
TATTTATACCCATAGGTGTCCCCTTGTCCAAGTAGAACTAGGGAAGCCAATATGGATACAATCCGAGTAGTCCTTGTCGTTCCATGTACAACTCTTGTTG

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	73.90%	15.10%	7.45%	3.53%	NA
All Indica	2759	62.60%	25.20%	11.78%	0.43%	NA
All Japonica	1512	98.40%	0.40%	0.20%	0.99%	NA
Aus	269	42.00%	0.70%	7.06%	50.19%	NA
Indica I	595	44.00%	31.40%	24.54%	0.00%	NA
Indica II	465	84.70%	7.50%	7.10%	0.65%	NA
Indica III	913	68.70%	26.70%	4.38%	0.22%	NA
Indica Intermediate	786	56.50%	29.10%	13.49%	0.89%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	95.80%	0.80%	0.40%	2.98%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	82.20%	11.10%	4.44%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0324328837	C -> T	LOC_Os03g43560.1	downstream_gene_variant ; 465.0bp to feature; MODIFIER	silent_mutation	Average:38.933; most accessible tissue: Minghui63 flag leaf, score: 55.068	N	N	N	N
vg0324328837	C -> T	LOC_Os03g43560-LOC_Os03g43564	intergenic_region ; MODIFIER	silent_mutation	Average:38.933; most accessible tissue: Minghui63 flag leaf, score: 55.068	N	N	N	N
vg0324328837	C -> DEL	N	N	silent_mutation	Average:38.933; most accessible tissue: Minghui63 flag leaf, score: 55.068	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324328837	2.56E-06	1.12E-07	mr1574	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
vg0324328837	NA	8.02E-06	mr1542_2	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
vg0324328837	NA	8.12E-06	mr1992_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