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Detailed information for vg0327530071:

Variant ID: vg0327530071 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27530071
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGTGTGAAGCCTATTAATTTCACAGTAAACACACAAAGCTACCCACACAAGCGCTCCAGACTATCCTTCTTACTTGGCTGTTCTCGTGTTGGGGGCTA[G/A]
ATATACTCGGGCCATTCCCACGAGGACAGGGCGGCTACAGGTTCCTATTCGTGGCGATCGACAAATTCACAAAATGGATCGAGGCGATACCCACGGGGGA

Reverse complement sequence

TCCCCCGTGGGTATCGCCTCGATCCATTTTGTGAATTTGTCGATCGCCACGAATAGGAACCTGTAGCCGCCCTGTCCTCGTGGGAATGGCCCGAGTATAT[C/T]
TAGCCCCCAACACGAGAACAGCCAAGTAAGAAGGATAGTCTGGAGCGCTTGTGTGGGTAGCTTTGTGTGTTTACTGTGAAATTAATAGGCTTCACACCGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.70%	10.40%	4.93%	0.00%	NA
All Indica	2759	76.10%	15.90%	7.94%	0.00%	NA
All Japonica	1512	99.60%	0.30%	0.07%	0.00%	NA
Aus	269	98.50%	1.10%	0.37%	0.00%	NA
Indica I	595	52.90%	39.80%	7.23%	0.00%	NA
Indica II	465	70.30%	10.10%	19.57%	0.00%	NA
Indica III	913	93.40%	3.80%	2.74%	0.00%	NA
Indica Intermediate	786	77.00%	15.40%	7.63%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	55.20%	35.40%	9.38%	0.00%	NA
Intermediate	90	85.60%	11.10%	3.33%	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
vg0327530071	G -> A	LOC_Os03g48350.1	splice_acceptor_variant&intron_variant ; HIGH	splice_acceptor_variant	Average:36.077; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327530071	3.78E-06	NA	mr1682	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