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Detailed information for vg0618478943:

Variant ID: vg0618478943 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18478943
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

AAGCTATACTTCAAATCAAGCAGTTACCCATTCCCGCTTGTGGTAAGCGCGGTAAATCTTCCACTGCATCCCGCGAACCAGTCATTAATTGCCATGGGTG[C/T]
GACTAGTAAAACCATGCATCCACAAGGCACCACTCAGTCGCATTTTAATTGGATAATTACGACCAATGAAACATGGCCACTTAATTTTAGTGGTAATTAA

Reverse complement sequence

TTAATTACCACTAAAATTAAGTGGCCATGTTTCATTGGTCGTAATTATCCAATTAAAATGCGACTGAGTGGTGCCTTGTGGATGCATGGTTTTACTAGTC[G/A]
CACCCATGGCAATTAATGACTGGTTCGCGGGATGCAGTGGAAGATTTACCGCGCTTACCACAAGCGGGAATGGGTAACTGCTTGATTTGAAGTATAGCTT

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	23.50%	7.00%	10.62%	58.82%	NA
All Indica	2759	6.00%	1.30%	8.77%	83.91%	NA
All Japonica	1512	60.80%	18.80%	12.63%	7.67%	NA
Aus	269	0.40%	0.00%	4.83%	94.80%	NA
Indica I	595	7.60%	0.50%	20.34%	71.60%	NA
Indica II	465	4.10%	2.60%	8.60%	84.73%	NA
Indica III	913	2.70%	0.90%	1.31%	95.07%	NA
Indica Intermediate	786	9.70%	1.80%	8.78%	79.77%	NA
Temperate Japonica	767	75.60%	0.50%	18.38%	5.48%	NA
Tropical Japonica	504	32.90%	52.40%	3.17%	11.51%	NA
Japonica Intermediate	241	72.20%	7.10%	14.11%	6.64%	NA
VI/Aromatic	96	2.10%	0.00%	45.83%	52.08%	NA
Intermediate	90	25.60%	12.20%	13.33%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618478943	C -> T	LOC_Os06g31810.1	upstream_gene_variant ; 4724.0bp to feature; MODIFIER	silent_mutation	Average:16.561; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0618478943	C -> T	LOC_Os06g31820.1	upstream_gene_variant ; 6.0bp to feature; MODIFIER	silent_mutation	Average:16.561; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0618478943	C -> T	LOC_Os06g31820-LOC_Os06g31830	intergenic_region ; MODIFIER	silent_mutation	Average:16.561; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0618478943	C -> DEL	N	N	silent_mutation	Average:16.561; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618478943	NA	4.21E-06	mr1852	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
vg0618478943	1.27E-06	NA	mr1925	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
vg0618478943	NA	2.29E-09	mr1993	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
vg0618478943	NA	2.43E-07	mr1408_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
vg0618478943	3.65E-06	4.10E-14	mr1993_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