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Detailed information for vg0412125261:

Variant ID: vg0412125261 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12125261
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

CACCTCCCGCCATTGCTCGTGCATCGCCAGCACCCATCGCCGGTGGTTGCATGTCGCTGCCCGTTGTTGGTATTTCTTAACATTACTATAAATATAATTC[C/T]
CAGCAATTGCGCAGTAATACTTCTAGTATATTATGGTTACAGAGTTCATTCGCAAGCGCACGGATATACCATTGTAGCATTTCAACCGAGAGTATTCCAA

Reverse complement sequence

TTGGAATACTCTCGGTTGAAATGCTACAATGGTATATCCGTGCGCTTGCGAATGAACTCTGTAACCATAATATACTAGAAGTATTACTGCGCAATTGCTG[G/A]
GAATTATATTTATAGTAATGTTAAGAAATACCAACAACGGGCAGCGACATGCAACCACCGGCGATGGGTGCTGGCGATGCACGAGCAATGGCGGGAGGTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.30%	25.30%	5.06%	19.36%	NA
All Indica	2759	78.90%	10.90%	8.16%	2.03%	NA
All Japonica	1512	1.80%	47.60%	0.40%	50.26%	NA
Aus	269	46.80%	52.00%	0.74%	0.37%	NA
Indica I	595	88.40%	0.80%	9.58%	1.18%	NA
Indica II	465	66.70%	24.10%	6.24%	3.01%	NA
Indica III	913	77.20%	12.50%	8.00%	2.30%	NA
Indica Intermediate	786	80.90%	8.90%	8.40%	1.78%	NA
Temperate Japonica	767	0.70%	80.20%	0.00%	19.17%	NA
Tropical Japonica	504	2.60%	4.00%	0.79%	92.66%	NA
Japonica Intermediate	241	3.70%	34.90%	0.83%	60.58%	NA
VI/Aromatic	96	7.30%	13.50%	0.00%	79.17%	NA
Intermediate	90	42.20%	26.70%	6.67%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412125261	C -> DEL	N	N	silent_mutation	Average:52.686; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg0412125261	C -> T	LOC_Os04g21450.1	downstream_gene_variant ; 1415.0bp to feature; MODIFIER	silent_mutation	Average:52.686; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg0412125261	C -> T	LOC_Os04g21430-LOC_Os04g21450	intergenic_region ; MODIFIER	silent_mutation	Average:52.686; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412125261	NA	7.06E-06	mr1174	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
vg0412125261	2.13E-06	2.13E-06	mr1347	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
vg0412125261	NA	1.04E-08	mr1299_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
vg0412125261	NA	1.23E-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
vg0412125261	NA	5.12E-08	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
vg0412125261	NA	2.37E-07	mr1804_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