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Detailed information for vg0406781341:

Variant ID: vg0406781341 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6781341
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.31, others allele: 0.00, population size: 42. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCCAAGTGTGACAAGAGTTTTAAGGAGCTCAAGAAGAAATTAGTGTCTGCTCCAGTTCTGATTTTGCCCGATCAGACGAAAGACTTCCAAGTATATTG[T/C]
GACGCGACCCGTCACGGGCTTGGATGTGTTCTAATGCAAGAGGGCAGAGTGGTCGCTTGTGCCTCACGACAGTTGCGTCCACATGAAGGAAACTATCCAA

Reverse complement sequence

TTGGATAGTTTCCTTCATGTGGACGCAACTGTCGTGAGGCACAAGCGACCACTCTGCCCTCTTGCATTAGAACACATCCAAGCCCGTGACGGGTCGCGTC[A/G]
CAATATACTTGGAAGTCTTTCGTCTGATCGGGCAAAATCAGAACTGGAGCAGACACTAATTTCTTCTTGAGCTCCTTAAAACTCTTGTCACACTTGGCTG

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	46.50%	30.20%	5.42%	17.86%	NA
All Indica	2759	24.20%	45.40%	7.65%	22.73%	NA
All Japonica	1512	91.20%	3.60%	0.60%	4.56%	NA
Aus	269	23.80%	33.80%	7.06%	35.32%	NA
Indica I	595	51.60%	32.60%	6.22%	9.58%	NA
Indica II	465	27.10%	42.60%	9.25%	21.08%	NA
Indica III	913	5.80%	53.00%	7.89%	33.30%	NA
Indica Intermediate	786	23.30%	47.80%	7.51%	21.37%	NA
Temperate Japonica	767	94.90%	3.10%	0.26%	1.69%	NA
Tropical Japonica	504	88.90%	2.80%	1.19%	7.14%	NA
Japonica Intermediate	241	84.20%	7.10%	0.41%	8.30%	NA
VI/Aromatic	96	34.40%	11.50%	11.46%	42.71%	NA
Intermediate	90	57.80%	22.20%	6.67%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406781341	T -> C	LOC_Os04g12290.1	upstream_gene_variant ; 4404.0bp to feature; MODIFIER	silent_mutation	Average:38.199; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0406781341	T -> C	LOC_Os04g12270.1	downstream_gene_variant ; 4866.0bp to feature; MODIFIER	silent_mutation	Average:38.199; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0406781341	T -> C	LOC_Os04g12280.1	intron_variant ; MODIFIER	silent_mutation	Average:38.199; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0406781341	T -> DEL	N	N	silent_mutation	Average:38.199; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406781341	NA	1.68E-06	mr1677	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
vg0406781341	NA	2.35E-21	mr1698	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
vg0406781341	NA	4.63E-07	mr1819_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