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Detailed information for vg0805973370:

Variant ID: vg0805973370 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5973370
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTACAGTATATTTTTTTTAAGTCACAGTGTAATTTATGAAACTTACATTGTAACTTTTGTAAGCTACAATGTAATTTTTTAATCTTTGCATGTAAGTTTT[G/A]
AAATTTATATTGGATTTTGTCTTTTTCTTGAAGATATGGTAATTTAGTGTTCATTATGGTGTTTTGAGTTGCTTTTTGCTTTTTACTGTGTCTATTGGAT

Reverse complement sequence

ATCCAATAGACACAGTAAAAAGCAAAAAGCAACTCAAAACACCATAATGAACACTAAATTACCATATCTTCAAGAAAAAGACAAAATCCAATATAAATTT[C/T]
AAAACTTACATGCAAAGATTAAAAAATTACATTGTAGCTTACAAAAGTTACAATGTAAGTTTCATAAATTACACTGTGACTTAAAAAAAATATACTGTAA

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	52.30%	42.70%	0.06%	4.93%	NA
All Indica	2759	78.70%	13.70%	0.11%	7.50%	NA
All Japonica	1512	4.80%	94.40%	0.00%	0.73%	NA
Aus	269	65.10%	30.50%	0.00%	4.46%	NA
Indica I	595	97.00%	1.50%	0.00%	1.51%	NA
Indica II	465	87.30%	10.10%	0.00%	2.58%	NA
Indica III	913	64.10%	22.60%	0.33%	13.03%	NA
Indica Intermediate	786	76.80%	14.60%	0.00%	8.52%	NA
Temperate Japonica	767	2.60%	97.10%	0.00%	0.26%	NA
Tropical Japonica	504	3.80%	95.00%	0.00%	1.19%	NA
Japonica Intermediate	241	14.10%	84.60%	0.00%	1.24%	NA
VI/Aromatic	96	14.60%	84.40%	0.00%	1.04%	NA
Intermediate	90	41.10%	56.70%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805973370	G -> A	LOC_Os08g10280.1	downstream_gene_variant ; 2619.0bp to feature; MODIFIER	silent_mutation	Average:65.774; most accessible tissue: Minghui63 root, score: 79.298	N	N	N	N
vg0805973370	G -> A	LOC_Os08g10270.1	intron_variant ; MODIFIER	silent_mutation	Average:65.774; most accessible tissue: Minghui63 root, score: 79.298	N	N	N	N
vg0805973370	G -> DEL	N	N	silent_mutation	Average:65.774; most accessible tissue: Minghui63 root, score: 79.298	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805973370	2.17E-08	2.17E-08	mr1197	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
vg0805973370	NA	2.05E-06	mr1914_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