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Detailed information for vg0818341901:

Variant ID: vg0818341901 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18341901
Reference Allele: T	Alternative Allele: C,A
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.29, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTGGTATATCATTGATTGCATGGTCTTCTAGGAAACAATCAAGTGTTGCTCAATCAACTGCTGAATCTGAATATATTGCTGCTGCTAGTTGTTGTTCA[T/C,A]
AGATTCTTTGGCTTTTATCTACTTTGAAAGATTATGGTCTTACTTTTGAGAAAGTATCTCTCTTTTGTGATAATACAAGTGCTATTAACATTGCTAAGAA

Reverse complement sequence

TTCTTAGCAATGTTAATAGCACTTGTATTATCACAAAAGAGAGATACTTTCTCAAAAGTAAGACCATAATCTTTCAAAGTAGATAAAAGCCAAAGAATCT[A/G,T]
TGAACAACAACTAGCAGCAGCAATATATTCAGATTCAGCAGTTGATTGAGCAACACTTGATTGTTTCCTAGAAGACCATGCAATCAATGATATACCAAGA

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	75.60%	19.60%	3.28%	1.54%	NA
All Indica	2759	70.30%	23.20%	5.18%	1.34%	NA
All Japonica	1512	87.70%	9.50%	0.46%	2.38%	NA
Aus	269	55.80%	42.80%	1.49%	0.00%	NA
Indica I	595	75.60%	4.70%	15.46%	4.20%	NA
Indica II	465	87.30%	9.90%	2.58%	0.22%	NA
Indica III	913	59.90%	38.90%	1.20%	0.00%	NA
Indica Intermediate	786	68.30%	26.70%	3.56%	1.40%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	69.80%	24.60%	0.79%	4.76%	NA
Japonica Intermediate	241	88.40%	5.40%	1.24%	4.98%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	80.00%	18.90%	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
vg0818341901	T -> C	LOC_Os08g29840.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:19.926; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0818341901	T -> C	LOC_Os08g29854.1	upstream_gene_variant ; 3964.0bp to feature; MODIFIER	silent_mutation	Average:19.926; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0818341901	T -> A	LOC_Os08g29840.1	splice_region_variant&intron_variant ; LOW	N	Average:19.926; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0818341901	T -> A	LOC_Os08g29854.1	upstream_gene_variant ; 3964.0bp to feature; MODIFIER	N	Average:19.926; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0818341901	T -> DEL	N	N	silent_mutation	Average:19.926; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818341901	1.00E-06	5.10E-09	mr1836	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
vg0818341901	3.50E-07	3.49E-07	mr1335_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