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Detailed information for vg0404560956:

Variant ID: vg0404560956 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4560956
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.10, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TTGAAAAAGTGTGGCAAGCCACAACTGTGGCAGCGAACCAAACACATGCCTAACAAACTGTGACAGCCACAAGTGTGGTGTGAAAAAGTGTGGCCATGAA[C/T]
CAAACACCCCCTAAGTATATTGTGAATTGAAATTGAAATATTGTAGGAAACATATCTCACATAACTGAGCTGACAAAACTAATGAGGAAAAATATTTGAG

Reverse complement sequence

CTCAAATATTTTTCCTCATTAGTTTTGTCAGCTCAGTTATGTGAGATATGTTTCCTACAATATTTCAATTTCAATTCACAATATACTTAGGGGGTGTTTG[G/A]
TTCATGGCCACACTTTTTCACACCACACTTGTGGCTGTCACAGTTTGTTAGGCATGTGTTTGGTTCGCTGCCACAGTTGTGGCTTGCCACACTTTTTCAA

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	56.00%	33.60%	1.52%	8.89%	NA
All Indica	2759	43.80%	39.30%	2.32%	14.61%	NA
All Japonica	1512	74.40%	25.50%	0.07%	0.07%	NA
Aus	269	79.90%	14.50%	1.49%	4.09%	NA
Indica I	595	40.70%	6.20%	1.51%	51.60%	NA
Indica II	465	42.60%	49.20%	5.38%	2.80%	NA
Indica III	913	44.00%	53.30%	1.20%	1.42%	NA
Indica Intermediate	786	46.60%	42.10%	2.42%	8.91%	NA
Temperate Japonica	767	97.70%	2.30%	0.00%	0.00%	NA
Tropical Japonica	504	37.50%	62.30%	0.00%	0.20%	NA
Japonica Intermediate	241	77.60%	22.00%	0.41%	0.00%	NA
VI/Aromatic	96	56.20%	42.70%	1.04%	0.00%	NA
Intermediate	90	50.00%	42.20%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404560956	C -> DEL	N	N	silent_mutation	Average:36.274; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N
vg0404560956	C -> T	LOC_Os04g08460.1	downstream_gene_variant ; 1675.0bp to feature; MODIFIER	silent_mutation	Average:36.274; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N
vg0404560956	C -> T	LOC_Os04g08470.1	downstream_gene_variant ; 3447.0bp to feature; MODIFIER	silent_mutation	Average:36.274; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N
vg0404560956	C -> T	LOC_Os04g08460-LOC_Os04g08470	intergenic_region ; MODIFIER	silent_mutation	Average:36.274; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404560956	NA	1.22E-09	mr1593	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
vg0404560956	NA	1.81E-06	mr1668	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
vg0404560956	NA	2.65E-09	mr1036_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
vg0404560956	NA	1.50E-06	mr1036_2	Ind_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
vg0404560956	NA	6.47E-10	mr1062_2	Ind_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
vg0404560956	NA	5.37E-06	mr1169_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
vg0404560956	NA	5.04E-07	mr1842_2	Ind_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