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Detailed information for vg0404048007:

Variant ID: vg0404048007 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4048007
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.54, G: 0.47, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TCCGTCGCCACGCTAGCCGCCACCAGCCTCCACTGAGCCCACCGCCACCTTAAAAAGCCCCCTCAGGACCTCCTCCACCTTTTTCCCTATTTTTGCCACC[A/G]
TTCCTGAGCCCTATTCCGCTGCCGCGCCGTGTCCTAGCCGCCGCTGCCACATCTCCACCTCCGGCCGCTGCTAGTCGCCGCCCGGCTGCACCAATGCCAC

Reverse complement sequence

GTGGCATTGGTGCAGCCGGGCGGCGACTAGCAGCGGCCGGAGGTGGAGATGTGGCAGCGGCGGCTAGGACACGGCGCGGCAGCGGAATAGGGCTCAGGAA[T/C]
GGTGGCAAAAATAGGGAAAAAGGTGGAGGAGGTCCTGAGGGGGCTTTTTAAGGTGGCGGTGGGCTCAGTGGAGGCTGGTGGCGGCTAGCGTGGCGACGGA

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	41.90%	36.60%	0.47%	21.01%	NA
All Indica	2759	21.70%	46.70%	0.62%	30.99%	NA
All Japonica	1512	86.40%	9.70%	0.07%	3.77%	NA
Aus	269	8.90%	66.20%	0.74%	24.16%	NA
Indica I	595	47.40%	6.60%	0.84%	45.21%	NA
Indica II	465	25.80%	41.30%	1.29%	31.61%	NA
Indica III	913	2.50%	76.60%	0.22%	20.70%	NA
Indica Intermediate	786	22.10%	45.50%	0.51%	31.81%	NA
Temperate Japonica	767	97.10%	2.60%	0.00%	0.26%	NA
Tropical Japonica	504	76.20%	14.50%	0.20%	9.13%	NA
Japonica Intermediate	241	73.90%	22.40%	0.00%	3.73%	NA
VI/Aromatic	96	8.30%	89.60%	0.00%	2.08%	NA
Intermediate	90	47.80%	34.40%	2.22%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404048007	A -> DEL	N	N	silent_mutation	Average:49.071; most accessible tissue: Zhenshan97 young leaf, score: 91.967	N	N	N	N
vg0404048007	A -> G	LOC_Os04g07610.1	upstream_gene_variant ; 493.0bp to feature; MODIFIER	silent_mutation	Average:49.071; most accessible tissue: Zhenshan97 young leaf, score: 91.967	N	N	N	N
vg0404048007	A -> G	LOC_Os04g07600-LOC_Os04g07610	intergenic_region ; MODIFIER	silent_mutation	Average:49.071; most accessible tissue: Zhenshan97 young leaf, score: 91.967	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404048007	5.84E-07	NA	mr1698_2	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
vg0404048007	NA	5.24E-07	mr1698_2	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