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Detailed information for vg0401473114:

Variant ID: vg0401473114 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1473114
Reference Allele: T	Alternative Allele: G,C
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 47. )

Flanking Sequence (100 bp) in Reference Genome:

GAGCACGCCTGCAAGACACAAGGTTATTGCACCACAGGTGTGTGCATGACCAAACCGCTCGCCTGAGTTATCATGGTTAAAGTGCCTTCCTCCGCTACAA[T/G,C]
CTGCATCAAGACGGAGGAGAAATCAATAATCAAATGTGACCATGCCACCGCTCCAGAGATTTCAACATATACATCATGCTGGCGGTAAGTGCACTCAGGT

Reverse complement sequence

ACCTGAGTGCACTTACCGCCAGCATGATGTATATGTTGAAATCTCTGGAGCGGTGGCATGGTCACATTTGATTATTGATTTCTCCTCCGTCTTGATGCAG[A/C,G]
TTGTAGCGGAGGAAGGCACTTTAACCATGATAACTCAGGCGAGCGGTTTGGTCATGCACACACCTGTGGTGCAATAACCTTGTGTCTTGCAGGCGTGCTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.40%	22.60%	12.74%	34.24%	C: 0.04%
All Indica	2759	23.20%	32.50%	15.73%	28.52%	C: 0.07%
All Japonica	1512	46.90%	7.90%	6.28%	38.96%	NA
Aus	269	17.10%	2.60%	9.67%	70.63%	NA
Indica I	595	49.10%	10.80%	6.39%	33.78%	NA
Indica II	465	26.50%	43.90%	12.26%	17.42%	NA
Indica III	913	5.60%	40.40%	22.56%	31.22%	C: 0.22%
Indica Intermediate	786	22.00%	33.10%	16.92%	27.99%	NA
Temperate Japonica	767	70.90%	5.00%	3.78%	20.34%	NA
Tropical Japonica	504	11.50%	11.90%	6.75%	69.84%	NA
Japonica Intermediate	241	44.40%	8.70%	13.28%	33.61%	NA
VI/Aromatic	96	10.40%	24.00%	34.38%	31.25%	NA
Intermediate	90	36.70%	23.30%	15.56%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401473114	T -> C	LOC_Os04g03420.1	upstream_gene_variant ; 3840.0bp to feature; MODIFIER	silent_mutation	Average:7.383; most accessible tissue: Callus, score: 33.575	N	N	N	N
vg0401473114	T -> C	LOC_Os04g03440.1	upstream_gene_variant ; 4695.0bp to feature; MODIFIER	silent_mutation	Average:7.383; most accessible tissue: Callus, score: 33.575	N	N	N	N
vg0401473114	T -> C	LOC_Os04g03430.1	downstream_gene_variant ; 892.0bp to feature; MODIFIER	silent_mutation	Average:7.383; most accessible tissue: Callus, score: 33.575	N	N	N	N
vg0401473114	T -> C	LOC_Os04g03430-LOC_Os04g03440	intergenic_region ; MODIFIER	silent_mutation	Average:7.383; most accessible tissue: Callus, score: 33.575	N	N	N	N
vg0401473114	T -> DEL	N	N	silent_mutation	Average:7.383; most accessible tissue: Callus, score: 33.575	N	N	N	N
vg0401473114	T -> G	LOC_Os04g03420.1	upstream_gene_variant ; 3840.0bp to feature; MODIFIER	silent_mutation	Average:7.383; most accessible tissue: Callus, score: 33.575	N	N	N	N
vg0401473114	T -> G	LOC_Os04g03440.1	upstream_gene_variant ; 4695.0bp to feature; MODIFIER	silent_mutation	Average:7.383; most accessible tissue: Callus, score: 33.575	N	N	N	N
vg0401473114	T -> G	LOC_Os04g03430.1	downstream_gene_variant ; 892.0bp to feature; MODIFIER	silent_mutation	Average:7.383; most accessible tissue: Callus, score: 33.575	N	N	N	N
vg0401473114	T -> G	LOC_Os04g03430-LOC_Os04g03440	intergenic_region ; MODIFIER	silent_mutation	Average:7.383; most accessible tissue: Callus, score: 33.575	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401473114	NA	2.51E-06	mr1544_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