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Detailed information for vg0402214005:

Variant ID: vg0402214005 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2214005
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, A: 0.08, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

TGTCGTGGGCAGATGATTTTTTTTTAATTCTAGCAGCAGATTTCAGTGTACATTGAGAACATCAAGTGTCAAATATCACCAATCCTTCAAATAAGTCAGG[A/C]
ATTCATTTCCTAAATCGCATTGAACATAAGCATGTAGTTTTAACAGTTAAAGTGTCGATGCTTCAGAGAAAGTACTCAGTATTTTATGACTGATCTTATT

Reverse complement sequence

AATAAGATCAGTCATAAAATACTGAGTACTTTCTCTGAAGCATCGACACTTTAACTGTTAAAACTACATGCTTATGTTCAATGCGATTTAGGAAATGAAT[T/G]
CCTGACTTATTTGAAGGATTGGTGATATTTGACACTTGATGTTCTCAATGTACACTGAAATCTGCTGCTAGAATTAAAAAAAAATCATCTGCCCACGACA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.90%	15.80%	1.14%	48.12%	NA
All Indica	2759	21.10%	17.50%	1.63%	59.77%	NA
All Japonica	1512	66.40%	0.30%	0.40%	32.87%	NA
Aus	269	3.00%	86.60%	0.37%	10.04%	NA
Indica I	595	6.60%	20.80%	1.51%	71.09%	NA
Indica II	465	4.90%	4.10%	1.94%	89.03%	NA
Indica III	913	36.80%	19.90%	1.10%	42.17%	NA
Indica Intermediate	786	23.30%	20.20%	2.16%	54.33%	NA
Temperate Japonica	767	95.40%	0.10%	0.00%	4.43%	NA
Tropical Japonica	504	29.40%	0.20%	0.79%	69.64%	NA
Japonica Intermediate	241	51.50%	1.20%	0.83%	46.47%	NA
VI/Aromatic	96	25.00%	11.50%	2.08%	61.46%	NA
Intermediate	90	36.70%	16.70%	0.00%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402214005	A -> C	LOC_Os04g04620.1	downstream_gene_variant ; 2152.0bp to feature; MODIFIER	silent_mutation	Average:11.188; most accessible tissue: Callus, score: 67.571	N	N	N	N
vg0402214005	A -> C	LOC_Os04g04610-LOC_Os04g04620	intergenic_region ; MODIFIER	silent_mutation	Average:11.188; most accessible tissue: Callus, score: 67.571	N	N	N	N
vg0402214005	A -> DEL	N	N	silent_mutation	Average:11.188; most accessible tissue: Callus, score: 67.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402214005	6.88E-06	2.00E-07	mr1498_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
vg0402214005	4.10E-06	4.10E-06	mr1925_2	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