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Detailed information for vg0403421977:

Variant ID: vg0403421977 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3421977
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.40, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

TTGATAAATGTAAGAATCATAATTATTTATGTATTATGTTTACATTATTGTTCCTAATTCTTAAAATCACAACCCACGATGAATTCGGCTAGCTGGGTTC[G/A]
TGATTCTCAGTCCAAATCATCGACCCAGGGTCATCGACCTGCATGACATGGAGTCATGTCCCTCGACCGATACTTTCGAACTGGGATCATCGTCCCAGCT

Reverse complement sequence

AGCTGGGACGATGATCCCAGTTCGAAAGTATCGGTCGAGGGACATGACTCCATGTCATGCAGGTCGATGACCCTGGGTCGATGATTTGGACTGAGAATCA[C/T]
GAACCCAGCTAGCCGAATTCATCGTGGGTTGTGATTTTAAGAATTAGGAACAATAATGTAAACATAATACATAAATAATTATGATTCTTACATTTATCAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.40%	17.80%	0.53%	12.34%	NA
All Indica	2759	84.90%	8.70%	0.40%	5.98%	NA
All Japonica	1512	43.80%	28.50%	0.86%	26.79%	NA
Aus	269	59.10%	39.80%	0.37%	0.74%	NA
Indica I	595	91.10%	3.90%	0.34%	4.71%	NA
Indica II	465	88.40%	9.20%	0.43%	1.94%	NA
Indica III	913	84.70%	8.20%	0.55%	6.57%	NA
Indica Intermediate	786	78.40%	12.70%	0.25%	8.65%	NA
Temperate Japonica	767	61.80%	30.10%	0.65%	7.43%	NA
Tropical Japonica	504	19.00%	24.00%	1.39%	55.56%	NA
Japonica Intermediate	241	38.60%	32.80%	0.41%	28.22%	NA
VI/Aromatic	96	50.00%	49.00%	0.00%	1.04%	NA
Intermediate	90	73.30%	15.60%	0.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403421977	G -> DEL	N	N	silent_mutation	Average:65.315; most accessible tissue: Minghui63 panicle, score: 93.294	N	N	N	N
vg0403421977	G -> A	LOC_Os04g06510.1	downstream_gene_variant ; 2230.0bp to feature; MODIFIER	silent_mutation	Average:65.315; most accessible tissue: Minghui63 panicle, score: 93.294	N	N	N	N
vg0403421977	G -> A	LOC_Os04g06500.1	downstream_gene_variant ; 2488.0bp to feature; MODIFIER	silent_mutation	Average:65.315; most accessible tissue: Minghui63 panicle, score: 93.294	N	N	N	N
vg0403421977	G -> A	LOC_Os04g06510-LOC_Os04g06500	intergenic_region ; MODIFIER	silent_mutation	Average:65.315; most accessible tissue: Minghui63 panicle, score: 93.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403421977	7.51E-08	NA	Awn_length	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0403421977	NA	2.11E-06	mr1757_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