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Detailed information for vg0610852428:

Variant ID: vg0610852428 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10852428
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGGGTACGATATCGGTGGATATAGGTTTTACACGATGTTCAAGGTCAAGAAAAGCGCAGCTCAGAACAGCGGAGTTCGGGTGGAGGCGTTTGACGCAT[C/A]
AGATGAGAAGAAGTCTTACTACGGGATCATACAGGACATTTGGGAGCTGGACTATGGCCTTAACATACAGATCCCGGTGCTACGATGCCAATGGGTCAGA

Reverse complement sequence

TCTGACCCATTGGCATCGTAGCACCGGGATCTGTATGTTAAGGCCATAGTCCAGCTCCCAAATGTCCTGTATGATCCCGTAGTAAGACTTCTTCTCATCT[G/T]
ATGCGTCAAACGCCTCCACCCGAACTCCGCTGTTCTGAGCTGCGCTTTTCTTGACCTTGAACATCGTGTAAAACCTATATCCACCGATATCGTACCCTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.80%	1.50%	27.21%	2.45%	NA
All Indica	2759	51.10%	2.50%	42.23%	4.17%	NA
All Japonica	1512	94.00%	0.00%	5.89%	0.07%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	31.80%	3.70%	57.31%	7.23%	NA
Indica II	465	32.50%	2.20%	53.98%	11.40%	NA
Indica III	913	71.10%	1.10%	27.38%	0.44%	NA
Indica Intermediate	786	53.40%	3.60%	41.09%	1.91%	NA
Temperate Japonica	767	97.00%	0.00%	3.00%	0.00%	NA
Tropical Japonica	504	89.50%	0.00%	10.32%	0.20%	NA
Japonica Intermediate	241	94.20%	0.00%	5.81%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	65.60%	1.10%	33.33%	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
vg0610852428	C -> A	LOC_Os06g19080.1	stop_gained ; p.Ser827*; HIGH	stop_gained	Average:17.298; most accessible tissue: Callus, score: 55.285	N	N	N	N
vg0610852428	C -> DEL	LOC_Os06g19080.1	N	frameshift_variant	Average:17.298; most accessible tissue: Callus, score: 55.285	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610852428	NA	6.40E-06	mr1346	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
vg0610852428	3.66E-06	NA	mr1577	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
vg0610852428	5.92E-07	1.78E-06	mr1577	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
vg0610852428	NA	3.59E-06	mr1780	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