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Detailed information for vg0401347470:

Variant ID: vg0401347470 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1347470
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAGTATATCTTCACCTAGCTAGATCTAAACATGAGGCAGTGAAGATGGTTGGAATTAATTAAGGATTATGACATGGGAATTCATTATCACCCGAGAAA[G/A]
GCTAATGTTGTAGCAGATGCTCTCAGCAAGAAAGGCTATTGCAATGCTACGGAAGGACGCCAGTTGCCGTGGAAGTTATGCAAGGAATTTGAAAGATTGA

Reverse complement sequence

TCAATCTTTCAAATTCCTTGCATAACTTCCACGGCAACTGGCGTCCTTCCGTAGCATTGCAATAGCCTTTCTTGCTGAGAGCATCTGCTACAACATTAGC[C/T]
TTTCTCGGGTGATAATGAATTCCCATGTCATAATCCTTAATTAATTCCAACCATCTTCACTGCCTCATGTTTAGATCTAGCTAGGTGAAGATATACTTCA

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	48.60%	13.70%	28.97%	8.65%	NA
All Indica	2759	58.40%	5.60%	34.83%	1.12%	NA
All Japonica	1512	30.80%	30.60%	14.75%	23.94%	NA
Aus	269	43.50%	7.10%	48.70%	0.74%	NA
Indica I	595	40.70%	4.40%	53.78%	1.18%	NA
Indica II	465	50.10%	4.90%	43.44%	1.51%	NA
Indica III	913	72.30%	6.70%	20.37%	0.66%	NA
Indica Intermediate	786	60.70%	5.70%	32.19%	1.40%	NA
Temperate Japonica	767	5.50%	49.80%	6.00%	38.72%	NA
Tropical Japonica	504	63.70%	3.80%	26.79%	5.75%	NA
Japonica Intermediate	241	42.30%	25.30%	17.43%	14.94%	NA
VI/Aromatic	96	63.50%	0.00%	23.96%	12.50%	NA
Intermediate	90	48.90%	14.40%	34.44%	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
vg0401347470	G -> DEL	N	N	silent_mutation	Average:15.804; most accessible tissue: Callus, score: 47.748	N	N	N	N
vg0401347470	G -> A	LOC_Os04g03200.1	downstream_gene_variant ; 4672.0bp to feature; MODIFIER	silent_mutation	Average:15.804; most accessible tissue: Callus, score: 47.748	N	N	N	N
vg0401347470	G -> A	LOC_Os04g03190.1	intron_variant ; MODIFIER	silent_mutation	Average:15.804; most accessible tissue: Callus, score: 47.748	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401347470	NA	3.21E-07	mr1013	Jap_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
vg0401347470	NA	1.33E-06	mr1031	Jap_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
vg0401347470	3.54E-06	4.59E-08	mr1034	Jap_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
vg0401347470	NA	9.66E-07	mr1056	Jap_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