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Detailed information for vg0404929690:

Variant ID: vg0404929690 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4929690
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.27, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGTGACTGGAAAACAACCAAAGCAAGCTAACCCGAAGAAGAAAACATCCAGTCGTCCAATACCAAAAATCAGGAAGTCATCCAGGTACAAGTCATTTA[A/G]
TAATCTTCCCTGTATCGCTAAACATACACCATCAAAGTAGTGTTAATAGCATATCTCAAATCTGTAGGAAGCCATCTGACATCGATCCTTCTGGAAAAGA

Reverse complement sequence

TCTTTTCCAGAAGGATCGATGTCAGATGGCTTCCTACAGATTTGAGATATGCTATTAACACTACTTTGATGGTGTATGTTTAGCGATACAGGGAAGATTA[T/C]
TAAATGACTTGTACCTGGATGACTTCCTGATTTTTGGTATTGGACGACTGGATGTTTTCTTCTTCGGGTTAGCTTGCTTTGGTTGTTTTCCAGTCACCTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.60%	28.70%	4.04%	16.74%	NA
All Indica	2759	71.30%	8.60%	4.86%	15.22%	NA
All Japonica	1512	4.00%	70.40%	2.84%	22.75%	NA
Aus	269	85.10%	4.10%	4.83%	5.95%	NA
Indica I	595	93.60%	5.50%	0.00%	0.84%	NA
Indica II	465	59.10%	14.20%	3.44%	23.23%	NA
Indica III	913	65.70%	5.60%	9.86%	18.84%	NA
Indica Intermediate	786	68.20%	11.10%	3.56%	17.18%	NA
Temperate Japonica	767	1.40%	87.70%	0.91%	9.91%	NA
Tropical Japonica	504	6.70%	53.40%	4.76%	35.12%	NA
Japonica Intermediate	241	6.20%	51.00%	4.98%	37.76%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	55.60%	31.10%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404929690	A -> DEL	N	N	silent_mutation	Average:23.147; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0404929690	A -> G	LOC_Os04g09260.1	upstream_gene_variant ; 4151.0bp to feature; MODIFIER	silent_mutation	Average:23.147; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0404929690	A -> G	LOC_Os04g09284.1	downstream_gene_variant ; 2273.0bp to feature; MODIFIER	silent_mutation	Average:23.147; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0404929690	A -> G	LOC_Os04g09270.1	intron_variant ; MODIFIER	silent_mutation	Average:23.147; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404929690	NA	2.24E-06	mr1188_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