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Detailed information for vg0402977601:

Variant ID: vg0402977601 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2977601
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

GGTTTCAGTATGAGTCTCCTGGATTCTGTTGCAGGCAGGGGAAAATAAATGTACATGTTCCAGAAATCCTTGCCGAGTTAATACGGTTGTTTACCAGTCA[A/G]
GTGCATAATGATGCAAAGTATTTTAGAAAGCACATACGGTATTTCAACTCCCATTTCTCATTCACGAGCCTTGGAGTTACCCTTGACCAACGAGTCAGCA

Reverse complement sequence

TGCTGACTCGTTGGTCAAGGGTAACTCCAAGGCTCGTGAATGAGAAATGGGAGTTGAAATACCGTATGTGCTTTCTAAAATACTTTGCATCATTATGCAC[T/C]
TGACTGGTAAACAACCGTATTAACTCGGCAAGGATTTCTGGAACATGTACATTTATTTTCCCCTGCCTGCAACAGAATCCAGGAGACTCATACTGAAACC

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	44.20%	3.30%	4.66%	47.80%	NA
All Indica	2759	39.60%	5.50%	6.27%	48.68%	NA
All Japonica	1512	56.20%	0.30%	2.58%	40.94%	NA
Aus	269	15.60%	0.00%	2.23%	82.16%	NA
Indica I	595	25.70%	7.20%	4.87%	62.18%	NA
Indica II	465	33.10%	2.60%	6.88%	57.42%	NA
Indica III	913	50.50%	7.10%	8.98%	33.41%	NA
Indica Intermediate	786	41.20%	3.90%	3.82%	51.02%	NA
Temperate Japonica	767	76.50%	0.10%	2.09%	21.25%	NA
Tropical Japonica	504	29.00%	0.40%	3.37%	67.26%	NA
Japonica Intermediate	241	48.50%	0.40%	2.49%	48.55%	NA
VI/Aromatic	96	56.20%	1.00%	0.00%	42.71%	NA
Intermediate	90	58.90%	0.00%	2.22%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402977601	A -> DEL	N	N	silent_mutation	Average:8.731; most accessible tissue: Callus, score: 24.665	N	N	N	N
vg0402977601	A -> G	LOC_Os04g05790.1	upstream_gene_variant ; 3639.0bp to feature; MODIFIER	silent_mutation	Average:8.731; most accessible tissue: Callus, score: 24.665	N	N	N	N
vg0402977601	A -> G	LOC_Os04g05800.1	intron_variant ; MODIFIER	silent_mutation	Average:8.731; most accessible tissue: Callus, score: 24.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402977601	3.27E-06	NA	mr1364_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
vg0402977601	NA	1.80E-06	mr1982_2	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