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Detailed information for vg0121827646:

Variant ID: vg0121827646 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21827646
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

ACATGCATGGTCCGCCGATGGTGTGGTTTCTTTGGGCCGGATGACAGGTGGGTCCCACGTGATATGTGGATCCAAGATTAAAGGATTGAAGATGAAACTC[A/G]
TATTTTTTATATTAGTACAGAAGAAATCAAAAGAATAGCATATTAATTCTAAAAAACAAGAATGACATAGAGATGATAAGGATGATGGGTGTAGACTAAC

Reverse complement sequence

GTTAGTCTACACCCATCATCCTTATCATCTCTATGTCATTCTTGTTTTTTAGAATTAATATGCTATTCTTTTGATTTCTTCTGTACTAATATAAAAAATA[T/C]
GAGTTTCATCTTCAATCCTTTAATCTTGGATCCACATATCACGTGGGACCCACCTGTCATCCGGCCCAAAGAAACCACACCATCGGCGGACCATGCATGT

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	40.60%	37.60%	0.13%	21.71%	NA
All Indica	2759	7.70%	59.90%	0.11%	32.33%	NA
All Japonica	1512	99.30%	0.50%	0.00%	0.20%	NA
Aus	269	33.50%	23.00%	0.74%	42.75%	NA
Indica I	595	1.30%	91.80%	0.17%	6.72%	NA
Indica II	465	2.80%	90.50%	0.00%	6.67%	NA
Indica III	913	6.90%	26.80%	0.22%	66.05%	NA
Indica Intermediate	786	16.30%	56.00%	0.00%	27.74%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	0.60%	0.00%	0.40%	NA
Japonica Intermediate	241	97.90%	1.70%	0.00%	0.41%	NA
VI/Aromatic	96	65.60%	24.00%	1.04%	9.38%	NA
Intermediate	90	55.60%	36.70%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121827646	A -> G	LOC_Os01g38890.1	upstream_gene_variant ; 1415.0bp to feature; MODIFIER	silent_mutation	Average:43.097; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N
vg0121827646	A -> G	LOC_Os01g38890-LOC_Os01g38900	intergenic_region ; MODIFIER	silent_mutation	Average:43.097; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N
vg0121827646	A -> DEL	N	N	silent_mutation	Average:43.097; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121827646	7.17E-07	NA	mr1322	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
vg0121827646	NA	1.76E-06	mr1338	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
vg0121827646	NA	3.87E-09	mr1352	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