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Detailed information for vg0802210939:

Variant ID: vg0802210939 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2210939
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTACTCCTTTCGTCCTAAAATATAACAACTTTTAGCTCTCAAGATTTGTCCCAAAATATAACAACTTCTCCATCAACATTCTCTTCCCAACCAATCACAA[C/A]
TCTCCACCATTCACTTTTCCCACCTACCTTCACTATTTAATCAATTACAACCCTCCACCATTCACTTCTACTTGCTTTCTTAATAACCGTGTCTAACTCT

Reverse complement sequence

AGAGTTAGACACGGTTATTAAGAAAGCAAGTAGAAGTGAATGGTGGAGGGTTGTAATTGATTAAATAGTGAAGGTAGGTGGGAAAAGTGAATGGTGGAGA[G/T]
TTGTGATTGGTTGGGAAGAGAATGTTGATGGAGAAGTTGTTATATTTTGGGACAAATCTTGAGAGCTAAAAGTTGTTATATTTTAGGACGAAAGGAGTAA

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	79.00%	19.10%	1.46%	0.47%	NA
All Indica	2759	67.10%	32.00%	0.87%	0.00%	NA
All Japonica	1512	99.70%	0.20%	0.07%	0.00%	NA
Aus	269	75.80%	0.00%	15.99%	8.18%	NA
Indica I	595	61.30%	38.30%	0.34%	0.00%	NA
Indica II	465	85.60%	14.20%	0.22%	0.00%	NA
Indica III	913	69.40%	30.20%	0.33%	0.00%	NA
Indica Intermediate	786	57.80%	39.90%	2.29%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	1.11%	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
vg0802210939	C -> A	LOC_Os08g04490.1	downstream_gene_variant ; 1250.0bp to feature; MODIFIER	silent_mutation	Average:38.33; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0802210939	C -> A	LOC_Os08g04500.1	intron_variant ; MODIFIER	silent_mutation	Average:38.33; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0802210939	C -> A	LOC_Os08g04500.2	intron_variant ; MODIFIER	silent_mutation	Average:38.33; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0802210939	C -> DEL	N	N	silent_mutation	Average:38.33; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802210939	NA	3.65E-07	mr1593	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
vg0802210939	8.31E-43	7.83E-68	mr1739	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
vg0802210939	9.72E-37	1.13E-65	mr1739	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
vg0802210939	NA	1.10E-06	mr1268_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
vg0802210939	3.84E-46	9.97E-68	mr1739_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
vg0802210939	1.79E-43	6.86E-76	mr1739_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