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Detailed information for vg0408412077:

Variant ID: vg0408412077 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8412077
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AGCGTCGAAAGCTAGTCGTCGGTTGCGATGTTGATGGAGGTGGGGAAGGAGCGGTTGGTGGTGACGGAGTGGCGACGAACGGGGCCGGCAGCGACTCCAT[C/G]
TCCAGTGGGAGTTCACACGGCTCGCCGGGCATTGTCACCACCGCCGTCCATCCATGGTAGGCACAATACTGTACCCCTTGCACAAGGATCCGGCGAGGTT

Reverse complement sequence

AACCTCGCCGGATCCTTGTGCAAGGGGTACAGTATTGTGCCTACCATGGATGGACGGCGGTGGTGACAATGCCCGGCGAGCCGTGTGAACTCCCACTGGA[G/C]
ATGGAGTCGCTGCCGGCCCCGTTCGTCGCCACTCCGTCACCACCAACCGCTCCTTCCCCACCTCCATCAACATCGCAACCGACGACTAGCTTTCGACGCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.60%	14.60%	10.92%	18.90%	NA
All Indica	2759	47.80%	23.50%	14.14%	14.57%	NA
All Japonica	1512	76.10%	0.10%	6.28%	17.46%	NA
Aus	269	17.80%	1.10%	7.06%	73.98%	NA
Indica I	595	50.30%	6.20%	17.14%	26.39%	NA
Indica II	465	48.20%	23.40%	12.26%	16.13%	NA
Indica III	913	43.80%	38.10%	12.38%	5.70%	NA
Indica Intermediate	786	50.50%	19.50%	15.01%	15.01%	NA
Temperate Japonica	767	98.00%	0.00%	0.39%	1.56%	NA
Tropical Japonica	504	39.10%	0.20%	15.48%	45.24%	NA
Japonica Intermediate	241	83.80%	0.40%	5.81%	9.96%	NA
VI/Aromatic	96	54.20%	27.10%	5.21%	13.54%	NA
Intermediate	90	61.10%	14.40%	7.78%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408412077	C -> DEL	N	N	silent_mutation	Average:37.872; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0408412077	C -> G	LOC_Os04g14960.1	upstream_gene_variant ; 3115.0bp to feature; MODIFIER	silent_mutation	Average:37.872; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0408412077	C -> G	LOC_Os04g14970.1	upstream_gene_variant ; 385.0bp to feature; MODIFIER	silent_mutation	Average:37.872; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0408412077	C -> G	LOC_Os04g14980.1	downstream_gene_variant ; 3926.0bp to feature; MODIFIER	silent_mutation	Average:37.872; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0408412077	C -> G	LOC_Os04g14970-LOC_Os04g14980	intergenic_region ; MODIFIER	silent_mutation	Average:37.872; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408412077	NA	1.07E-06	mr1946_2	Ind_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
vg0408412077	NA	1.07E-06	mr1948_2	Ind_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