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Detailed information for vg0431583357:

Variant ID: vg0431583357 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31583357
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CAGTTTACTGCCTTTTGTTCTGAAGTTTCTGCAGCGCTTCATACTGGGTACTTTTGAAGACTAATACACGCAGTGTAATTTGGTGTGAGTTTGTGTCTGC[A/C]
CTCTGCAGTGTGGATTTGTTGCTGTTTACTATTGGTAGTATTCTCTGGTTTCATTTGGCTAGTCGCACTCAACCGCTGCTGGACGGCGGACAGGTTAAGC

Reverse complement sequence

GCTTAACCTGTCCGCCGTCCAGCAGCGGTTGAGTGCGACTAGCCAAATGAAACCAGAGAATACTACCAATAGTAAACAGCAACAAATCCACACTGCAGAG[T/G]
GCAGACACAAACTCACACCAAATTACACTGCGTGTATTAGTCTTCAAAAGTACCCAGTATGAAGCGCTGCAGAAACTTCAGAACAAAAGGCAGTAAACTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.20%	17.50%	0.15%	2.18%	NA
All Indica	2759	83.70%	12.80%	0.18%	3.37%	NA
All Japonica	1512	78.20%	21.40%	0.07%	0.33%	NA
Aus	269	61.70%	38.30%	0.00%	0.00%	NA
Indica I	595	96.60%	2.50%	0.00%	0.84%	NA
Indica II	465	91.60%	5.40%	0.00%	3.01%	NA
Indica III	913	71.30%	23.40%	0.33%	4.93%	NA
Indica Intermediate	786	83.60%	12.50%	0.25%	3.69%	NA
Temperate Japonica	767	93.00%	6.40%	0.13%	0.52%	NA
Tropical Japonica	504	50.20%	49.80%	0.00%	0.00%	NA
Japonica Intermediate	241	89.60%	10.00%	0.00%	0.41%	NA
VI/Aromatic	96	61.50%	35.40%	0.00%	3.12%	NA
Intermediate	90	82.20%	14.40%	1.11%	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
vg0431583357	A -> C	LOC_Os04g53040.1	upstream_gene_variant ; 3228.0bp to feature; MODIFIER	silent_mutation	Average:51.215; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0431583357	A -> C	LOC_Os04g53030.1	intron_variant ; MODIFIER	silent_mutation	Average:51.215; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0431583357	A -> DEL	N	N	silent_mutation	Average:51.215; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431583357	2.18E-06	NA	mr1301	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