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Detailed information for vg0412124504:

Variant ID: vg0412124504 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12124504
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCAGTTTCAAGCAGATCGAAAACGAATCAATCAGTGCAGCCTGGTCCAGATTCACTAATTTAGTGCAGTCCGTACCAACCCTGTCCTTACTCGAGTAT[G/A]
TGCTTATGCAACATTTCCATACGGGTTTGGATAAGGAGTCTGCATTCTATCTGCACATAACCACTGGAGGATCGTTCATGCACAAAACACCGTCAGAAGG

Reverse complement sequence

CCTTCTGACGGTGTTTTGTGCATGAACGATCCTCCAGTGGTTATGTGCAGATAGAATGCAGACTCCTTATCCAAACCCGTATGGAAATGTTGCATAAGCA[C/T]
ATACTCGAGTAAGGACAGGGTTGGTACGGACTGCACTAAATTAGTGAATCTGGACCAGGCTGCACTGATTGATTCGTTTTCGATCTGCTTGAAACTGAGA

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	56.60%	24.90%	0.19%	18.37%	NA
All Indica	2759	89.30%	10.00%	0.07%	0.62%	NA
All Japonica	1512	1.90%	48.00%	0.20%	49.87%	NA
Aus	269	48.30%	50.60%	0.00%	1.12%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	75.70%	23.00%	0.22%	1.08%	NA
Indica III	913	87.60%	11.90%	0.00%	0.44%	NA
Indica Intermediate	786	91.30%	7.60%	0.13%	0.89%	NA
Temperate Japonica	767	0.80%	80.20%	0.13%	18.90%	NA
Tropical Japonica	504	2.60%	5.00%	0.20%	92.26%	NA
Japonica Intermediate	241	4.10%	35.70%	0.41%	59.75%	NA
VI/Aromatic	96	7.30%	13.50%	2.08%	77.08%	NA
Intermediate	90	48.90%	26.70%	2.22%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412124504	G -> DEL	N	N	silent_mutation	Average:53.445; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N
vg0412124504	G -> A	LOC_Os04g21430.1	upstream_gene_variant ; 4790.0bp to feature; MODIFIER	silent_mutation	Average:53.445; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N
vg0412124504	G -> A	LOC_Os04g21450.1	downstream_gene_variant ; 2172.0bp to feature; MODIFIER	silent_mutation	Average:53.445; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N
vg0412124504	G -> A	LOC_Os04g21430-LOC_Os04g21450	intergenic_region ; MODIFIER	silent_mutation	Average:53.445; most accessible tissue: Minghui63 young leaf, score: 65.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412124504	2.64E-06	2.64E-06	mr1347	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
vg0412124504	2.28E-06	2.28E-06	mr1366	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
vg0412124504	NA	6.65E-08	mr1514	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
vg0412124504	NA	1.77E-07	mr1321_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
vg0412124504	NA	1.19E-06	mr1727_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