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Detailed information for vg0402217448:

Variant ID: vg0402217448 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2217448
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, C: 0.17, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:

TTAATTAATTACTTGCCAACTAAAACTTGATAATGGTGGGTTGTGGGCACATGGTTTTGAGAGTTGTGCTCATGACAATTAAGTACCGGTTCACGAGTTT[C/T]
GGTTGTGAAACATTAATCGTGCCAACCACAAGCCAGCGTGGGCAACGGCTTTACCTTTTGTATAGCATGGTTTATTGCGGGACACCAGACTGAGAAGTGA

Reverse complement sequence

TCACTTCTCAGTCTGGTGTCCCGCAATAAACCATGCTATACAAAAGGTAAAGCCGTTGCCCACGCTGGCTTGTGGTTGGCACGATTAATGTTTCACAACC[G/A]
AAACTCGTGAACCGGTACTTAATTGTCATGAGCACAACTCTCAAAACCATGTGCCCACAACCCACCATTATCAAGTTTTAGTTGGCAAGTAATTAATTAA

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	33.90%	17.40%	19.00%	29.71%	NA
All Indica	2759	54.00%	3.30%	24.68%	17.98%	NA
All Japonica	1512	3.50%	46.00%	8.80%	41.73%	NA
Aus	269	4.80%	4.10%	14.87%	76.21%	NA
Indica I	595	60.00%	3.50%	14.62%	21.85%	NA
Indica II	465	60.40%	3.00%	14.62%	21.94%	NA
Indica III	913	48.70%	1.00%	36.04%	14.24%	NA
Indica Intermediate	786	51.90%	6.00%	25.06%	17.05%	NA
Temperate Japonica	767	1.70%	72.80%	3.91%	21.64%	NA
Tropical Japonica	504	6.00%	9.90%	14.48%	69.64%	NA
Japonica Intermediate	241	4.10%	36.10%	12.45%	47.30%	NA
VI/Aromatic	96	11.50%	11.50%	28.12%	48.96%	NA
Intermediate	90	40.00%	13.30%	18.89%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402217448	C -> DEL	N	N	silent_mutation	Average:14.8; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0402217448	C -> T	LOC_Os04g04620.1	upstream_gene_variant ; 875.0bp to feature; MODIFIER	silent_mutation	Average:14.8; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0402217448	C -> T	LOC_Os04g04640.1	downstream_gene_variant ; 3425.0bp to feature; MODIFIER	silent_mutation	Average:14.8; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0402217448	C -> T	LOC_Os04g04620-LOC_Os04g04640	intergenic_region ; MODIFIER	silent_mutation	Average:14.8; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402217448	NA	3.38E-06	mr1295_2	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
vg0402217448	3.29E-06	2.18E-08	mr1553_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
vg0402217448	1.27E-07	1.27E-07	mr1574_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
vg0402217448	3.22E-08	1.16E-09	mr1781_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
vg0402217448	NA	1.15E-06	mr1790_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
vg0402217448	NA	1.19E-06	mr1827_2	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
vg0402217448	2.23E-06	NA	mr1860_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