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Detailed information for vg0708820220:

Variant ID: vg0708820220 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8820220
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, A: 0.07, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CCCAAACGAAGCGAAGTTAGTACATTGGCACGCCACGAAGAGAAGGAATGATGGTATGCTTAGACAACTAGCGGATTCGATTGAATGGAGGAATATCGAT[C/A]
AAAAACACAAAGACTTTGCTGTCGACCCTAGAAACATGAGGATATGTCTATGTACGGATGGCATGAATCCTTTCGGTGACATGAGTAGTACTCACAGCAC

Reverse complement sequence

GTGCTGTGAGTACTACTCATGTCACCGAAAGGATTCATGCCATCCGTACATAGACATATCCTCATGTTTCTAGGGTCGACAGCAAAGTCTTTGTGTTTTT[G/T]
ATCGATATTCCTCCATTCAATCGAATCCGCTAGTTGTCTAAGCATACCATCATTCCTTCTCTTCGTGGCGTGCCAATGTACTAACTTCGCTTCGTTTGGG

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	93.30%	6.50%	0.15%	0.00%	NA
All Indica	2759	93.60%	6.40%	0.00%	0.00%	NA
All Japonica	1512	92.40%	7.10%	0.46%	0.00%	NA
Aus	269	94.80%	5.20%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	84.00%	16.00%	0.00%	0.00%	NA
Indica Intermediate	786	96.30%	3.70%	0.00%	0.00%	NA
Temperate Japonica	767	95.80%	3.40%	0.78%	0.00%	NA
Tropical Japonica	504	88.70%	11.30%	0.00%	0.00%	NA
Japonica Intermediate	241	89.20%	10.40%	0.41%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	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
vg0708820220	C -> A	LOC_Os07g15280.1	upstream_gene_variant ; 4972.0bp to feature; MODIFIER	silent_mutation	Average:26.358; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0708820220	C -> A	LOC_Os07g15300.1	upstream_gene_variant ; 4402.0bp to feature; MODIFIER	silent_mutation	Average:26.358; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0708820220	C -> A	LOC_Os07g15290.1	intron_variant ; MODIFIER	silent_mutation	Average:26.358; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708820220	NA	2.90E-08	mr1038_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
vg0708820220	2.59E-08	2.59E-08	mr1389_2	Jap_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