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Detailed information for vg0630443303:

Variant ID: vg0630443303 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 30443303
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

TGGCAGCGATATGGGCCAAGAGGAGGTTAGAGCCATGTGTCCAATGAAATGGTGACTTTATTATTATCTCACATCATGTATTTCTAAGATCATTTCATAT[A/G]
TAAATATATATAATTATTATATACATGTTTAGTTTACAAGTCATGCGGAATATTTAAATGTACTGTGCATTGTCTTATGTATGCAATAAAATGACTACAA

Reverse complement sequence

TTGTAGTCATTTTATTGCATACATAAGACAATGCACAGTACATTTAAATATTCCGCATGACTTGTAAACTAAACATGTATATAATAATTATATATATTTA[T/C]
ATATGAAATGATCTTAGAAATACATGATGTGAGATAATAATAAAGTCACCATTTCATTGGACACATGGCTCTAACCTCCTCTTGGCCCATATCGCTGCCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.40%	2.40%	19.97%	34.26%	NA
All Indica	2759	28.60%	3.70%	30.52%	37.22%	NA
All Japonica	1512	63.30%	0.40%	3.37%	32.94%	NA
Aus	269	88.50%	0.70%	9.29%	1.49%	NA
Indica I	595	46.60%	1.20%	13.95%	38.32%	NA
Indica II	465	6.70%	2.40%	29.03%	61.94%	NA
Indica III	913	27.40%	6.90%	43.81%	21.91%	NA
Indica Intermediate	786	29.30%	2.70%	28.50%	39.57%	NA
Temperate Japonica	767	93.50%	0.10%	0.39%	6.00%	NA
Tropical Japonica	504	19.00%	1.00%	8.33%	71.63%	NA
Japonica Intermediate	241	59.80%	0.00%	2.49%	37.76%	NA
VI/Aromatic	96	36.50%	0.00%	5.21%	58.33%	NA
Intermediate	90	36.70%	2.20%	23.33%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0630443303	A -> G	LOC_Os06g50290.1	downstream_gene_variant ; 71.0bp to feature; MODIFIER	silent_mutation	Average:8.893; most accessible tissue: Callus, score: 43.968	N	N	N	N
vg0630443303	A -> G	LOC_Os06g50300.1	downstream_gene_variant ; 1108.0bp to feature; MODIFIER	silent_mutation	Average:8.893; most accessible tissue: Callus, score: 43.968	N	N	N	N
vg0630443303	A -> G	LOC_Os06g50290-LOC_Os06g50300	intergenic_region ; MODIFIER	silent_mutation	Average:8.893; most accessible tissue: Callus, score: 43.968	N	N	N	N
vg0630443303	A -> DEL	N	N	silent_mutation	Average:8.893; most accessible tissue: Callus, score: 43.968	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0630443303	NA	5.63E-07	mr1064_2	Jap_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
vg0630443303	3.30E-06	NA	mr1124_2	Jap_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
vg0630443303	6.20E-06	1.23E-06	mr1312_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
vg0630443303	3.93E-07	2.49E-08	mr1663_2	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
vg0630443303	1.01E-06	NA	mr1665_2	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
vg0630443303	5.95E-06	NA	mr1687_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
vg0630443303	NA	6.37E-08	mr1952_2	Jap_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