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Detailed information for vg0420302986:

Variant ID: vg0420302986 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20302986
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.11, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TCAATTAAGGCAAAATTGGTTATATAGCATCGAAAGTTCACGTTTTTGGTTTTATAGCACCGAAAGTTACCGGTTCACTTTAATAGCACCCAAAGTTCAC[T/C]
ATGTTCCCATTTTTAACACTTCCGTCAATTCTTGATCGTTTTCCGTCCGTCTTGATCCAGCCACACACACGATATGACGTTTCTACCCCTCACAAGTACA

Reverse complement sequence

TGTACTTGTGAGGGGTAGAAACGTCATATCGTGTGTGTGGCTGGATCAAGACGGACGGAAAACGATCAAGAATTGACGGAAGTGTTAAAAATGGGAACAT[A/G]
GTGAACTTTGGGTGCTATTAAAGTGAACCGGTAACTTTCGGTGCTATAAAACCAAAAACGTGAACTTTCGATGCTATATAACCAATTTTGCCTTAATTGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.40%	22.10%	0.40%	1.12%	NA
All Indica	2759	94.50%	3.40%	0.18%	1.85%	NA
All Japonica	1512	43.70%	55.80%	0.53%	0.00%	NA
Aus	269	92.90%	4.50%	1.86%	0.74%	NA
Indica I	595	97.30%	2.70%	0.00%	0.00%	NA
Indica II	465	94.00%	4.90%	0.22%	0.86%	NA
Indica III	913	93.80%	2.10%	0.00%	4.16%	NA
Indica Intermediate	786	93.60%	4.70%	0.51%	1.15%	NA
Temperate Japonica	767	21.80%	77.20%	1.04%	0.00%	NA
Tropical Japonica	504	68.50%	31.50%	0.00%	0.00%	NA
Japonica Intermediate	241	61.40%	38.60%	0.00%	0.00%	NA
VI/Aromatic	96	35.40%	64.60%	0.00%	0.00%	NA
Intermediate	90	65.60%	33.30%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0420302986	T -> C	LOC_Os04g33560.1	upstream_gene_variant ; 1577.0bp to feature; MODIFIER	silent_mutation	Average:33.271; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0420302986	T -> C	LOC_Os04g33550-LOC_Os04g33560	intergenic_region ; MODIFIER	silent_mutation	Average:33.271; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0420302986	T -> DEL	N	N	silent_mutation	Average:33.271; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420302986	NA	1.65E-07	mr1040	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
vg0420302986	NA	3.86E-06	mr1977	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
vg0420302986	NA	2.08E-08	mr1045_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
vg0420302986	NA	2.39E-07	mr1748_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
vg0420302986	NA	4.60E-06	mr1763_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
vg0420302986	NA	2.05E-06	mr1785_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
vg0420302986	NA	1.66E-14	mr1902_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