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Detailed information for vg0807843997:

Variant ID: vg0807843997 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7843997
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGGAAAAGTTGTGAATCTCGAGCAAGTTGAAGGAGCAGGAGAAGAACAGGTTTCACAGGCAAGAGCAGAGCCACAGTAAGATGAAAAATGCTAAGTG[A/C]
ATCAAGTTACCAGACCGTTTTGTGGCAAGTATGCAACAATAAGTTGAAGAAAGACTAGCAGAGTCTGAAGCTGTGAAGGAGTCTGAAGATCCCTTTTTGG

Reverse complement sequence

CCAAAAAGGGATCTTCAGACTCCTTCACAGCTTCAGACTCTGCTAGTCTTTCTTCAACTTATTGTTGCATACTTGCCACAAAACGGTCTGGTAACTTGAT[T/G]
CACTTAGCATTTTTCATCTTACTGTGGCTCTGCTCTTGCCTGTGAAACCTGTTCTTCTCCTGCTCCTTCAACTTGCTCGAGATTCACAACTTTTCCATTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.10%	10.50%	11.02%	25.45%	NA
All Indica	2759	45.30%	17.20%	15.98%	21.57%	NA
All Japonica	1512	71.00%	0.30%	2.51%	26.19%	NA
Aus	269	41.30%	2.60%	10.41%	45.72%	NA
Indica I	595	24.00%	7.10%	10.76%	58.15%	NA
Indica II	465	44.70%	21.10%	29.68%	4.52%	NA
Indica III	913	65.40%	14.10%	11.83%	8.65%	NA
Indica Intermediate	786	38.30%	26.10%	16.67%	18.96%	NA
Temperate Japonica	767	60.00%	0.30%	3.52%	36.25%	NA
Tropical Japonica	504	83.30%	0.40%	1.19%	15.08%	NA
Japonica Intermediate	241	80.50%	0.00%	2.07%	17.43%	NA
VI/Aromatic	96	26.00%	1.00%	5.21%	67.71%	NA
Intermediate	90	54.40%	8.90%	10.00%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0807843997	A -> C	LOC_Os08g13190.1	downstream_gene_variant ; 19.0bp to feature; MODIFIER	silent_mutation	Average:35.375; most accessible tissue: Minghui63 young leaf, score: 67.374	N	N	N	N
vg0807843997	A -> C	LOC_Os08g13200.1	downstream_gene_variant ; 1958.0bp to feature; MODIFIER	silent_mutation	Average:35.375; most accessible tissue: Minghui63 young leaf, score: 67.374	N	N	N	N
vg0807843997	A -> C	LOC_Os08g13190-LOC_Os08g13200	intergenic_region ; MODIFIER	silent_mutation	Average:35.375; most accessible tissue: Minghui63 young leaf, score: 67.374	N	N	N	N
vg0807843997	A -> DEL	N	N	silent_mutation	Average:35.375; most accessible tissue: Minghui63 young leaf, score: 67.374	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807843997	3.33E-07	5.39E-08	mr1717_2	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