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Detailed information for vg0514271389:

Variant ID: vg0514271389 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14271389
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.12, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

GTCAAGGGTTGGTTGCACAACCTTAAACTTTATATATCAGTACCCGCCATTATCTATAGGGTTTGGGTTTTGCTTAGATTATTCTGTCGAGAACAGTTTC[A/G]
TCGCTAGATCGGTTTGTAAGACCCCAACTTGTGAGCTTAATCATTCATCTGCAATTTTGGTTGTATTCTACCTTGTTCTTGTTTGTGTTCTTCTATTCGC

Reverse complement sequence

GCGAATAGAAGAACACAAACAAGAACAAGGTAGAATACAACCAAAATTGCAGATGAATGATTAAGCTCACAAGTTGGGGTCTTACAAACCGATCTAGCGA[T/C]
GAAACTGTTCTCGACAGAATAATCTAAGCAAAACCCAAACCCTATAGATAATGGCGGGTACTGATATATAAAGTTTAAGGTTGTGCAACCAACCCTTGAC

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	86.90%	10.70%	0.95%	1.38%	NA
All Indica	2759	86.20%	11.10%	1.49%	1.20%	NA
All Japonica	1512	99.20%	0.60%	0.13%	0.07%	NA
Aus	269	21.60%	66.50%	0.74%	11.15%	NA
Indica I	595	80.30%	19.30%	0.00%	0.34%	NA
Indica II	465	98.90%	0.90%	0.00%	0.22%	NA
Indica III	913	80.50%	12.50%	4.38%	2.63%	NA
Indica Intermediate	786	89.80%	9.30%	0.13%	0.76%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.00%	1.40%	0.40%	0.20%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0514271389	A -> DEL	N	N	silent_mutation	Average:44.698; most accessible tissue: Zhenshan97 young leaf, score: 65.804	N	N	N	N
vg0514271389	A -> G	LOC_Os05g24670.1	downstream_gene_variant ; 2308.0bp to feature; MODIFIER	silent_mutation	Average:44.698; most accessible tissue: Zhenshan97 young leaf, score: 65.804	N	N	N	N
vg0514271389	A -> G	LOC_Os05g24660-LOC_Os05g24670	intergenic_region ; MODIFIER	silent_mutation	Average:44.698; most accessible tissue: Zhenshan97 young leaf, score: 65.804	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514271389	4.59E-06	NA	mr1927_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