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Detailed information for vg0322414125:

Variant ID: vg0322414125 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22414125
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, G: 0.03, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCCAAACTGAAAAGAGACAAACAAACTTGTCAGCATTTTACCATTAATCAATGTTTAGAAGCAGTACTAACAAAAGCACAAGCAACAAAGGGATGCTC[G/T]
ACATACAGTACGAATCAATCACATTATCAAATTCGTAATTTGTTCAGATGTATCTAGTGTCCTGATGGCTCATATATAGTAGAGTTTATATAGATGATAT

Reverse complement sequence

ATATCATCTATATAAACTCTACTATATATGAGCCATCAGGACACTAGATACATCTGAACAAATTACGAATTTGATAATGTGATTGATTCGTACTGTATGT[C/A]
GAGCATCCCTTTGTTGCTTGTGCTTTTGTTAGTACTGCTTCTAAACATTGATTAATGGTAAAATGCTGACAAGTTTGTTTGTCTCTTTTCAGTTTGGGCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.20%	31.60%	0.08%	0.11%	NA
All Indica	2759	98.30%	1.60%	0.04%	0.11%	NA
All Japonica	1512	8.70%	91.30%	0.07%	0.00%	NA
Aus	269	95.50%	4.50%	0.00%	0.00%	NA
Indica I	595	98.50%	1.30%	0.00%	0.17%	NA
Indica II	465	97.40%	2.60%	0.00%	0.00%	NA
Indica III	913	99.30%	0.50%	0.00%	0.11%	NA
Indica Intermediate	786	97.50%	2.30%	0.13%	0.13%	NA
Temperate Japonica	767	1.20%	98.70%	0.13%	0.00%	NA
Tropical Japonica	504	9.70%	90.30%	0.00%	0.00%	NA
Japonica Intermediate	241	30.30%	69.70%	0.00%	0.00%	NA
VI/Aromatic	96	76.00%	24.00%	0.00%	0.00%	NA
Intermediate	90	54.40%	41.10%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0322414125	G -> T	LOC_Os03g40310.1	intron_variant ; MODIFIER	silent_mutation	Average:78.587; most accessible tissue: Zhenshan97 panicle, score: 90.467	N	N	N	N
vg0322414125	G -> DEL	N	N	silent_mutation	Average:78.587; most accessible tissue: Zhenshan97 panicle, score: 90.467	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322414125	NA	8.18E-06	mr1066	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
vg0322414125	2.00E-06	2.00E-06	mr1066	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
vg0322414125	5.24E-07	NA	mr1750	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
vg0322414125	NA	8.90E-36	mr1828	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
vg0322414125	NA	3.73E-41	mr1873	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
vg0322414125	NA	2.59E-24	mr1350_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
vg0322414125	NA	2.45E-34	mr1448_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
vg0322414125	8.36E-07	NA	mr1750_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
vg0322414125	NA	2.41E-65	mr1828_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