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Detailed information for vg1125700572:

Variant ID: vg1125700572 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25700572
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.02, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGCATAATAGGATTGATAGGATACTCATGCTAACAAGTTGCAACTTCTTTTTCGGAAGCTCATCTCCAAAGAACACTAAAGTTAAGCGTGCTTGACCT[A/G]
GAGAAATCTAGGGATGGGTGACCGACTGGGAAGTCTTTCCCGGGTGCGCACGAGTGAGGACAAAGTGCGCAGAAAAGACTGGTGTTGGTTTGTGAGGGCA

Reverse complement sequence

TGCCCTCACAAACCAACACCAGTCTTTTCTGCGCACTTTGTCCTCACTCGTGCGCACCCGGGAAAGACTTCCCAGTCGGTCACCCATCCCTAGATTTCTC[T/C]
AGGTCAAGCACGCTTAACTTTAGTGTTCTTTGGAGATGAGCTTCCGAAAAAGAAGTTGCAACTTGTTAGCATGAGTATCCTATCAATCCTATTATGCCTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.40%	17.20%	6.88%	43.48%	NA
All Indica	2759	30.00%	24.20%	8.92%	36.90%	NA
All Japonica	1512	39.20%	3.00%	2.31%	55.49%	NA
Aus	269	27.10%	32.30%	12.64%	27.88%	NA
Indica I	595	59.00%	9.10%	8.91%	23.03%	NA
Indica II	465	35.70%	21.30%	2.80%	40.22%	NA
Indica III	913	13.30%	37.70%	9.97%	39.10%	NA
Indica Intermediate	786	24.00%	21.80%	11.32%	42.88%	NA
Temperate Japonica	767	61.30%	1.40%	3.00%	34.29%	NA
Tropical Japonica	504	11.90%	4.40%	1.59%	82.14%	NA
Japonica Intermediate	241	26.10%	5.00%	1.66%	67.22%	NA
VI/Aromatic	96	7.30%	5.20%	4.17%	83.33%	NA
Intermediate	90	35.60%	10.00%	6.67%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125700572	A -> DEL	N	N	silent_mutation	Average:24.745; most accessible tissue: Callus, score: 67.481	N	N	N	N
vg1125700572	A -> G	LOC_Os11g42660.1	downstream_gene_variant ; 549.0bp to feature; MODIFIER	silent_mutation	Average:24.745; most accessible tissue: Callus, score: 67.481	N	N	N	N
vg1125700572	A -> G	LOC_Os11g42670.1	downstream_gene_variant ; 2508.0bp to feature; MODIFIER	silent_mutation	Average:24.745; most accessible tissue: Callus, score: 67.481	N	N	N	N
vg1125700572	A -> G	LOC_Os11g42660-LOC_Os11g42670	intergenic_region ; MODIFIER	silent_mutation	Average:24.745; most accessible tissue: Callus, score: 67.481	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125700572	6.49E-06	6.49E-06	mr1208	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
vg1125700572	NA	3.43E-07	mr1403	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
vg1125700572	NA	7.48E-08	mr1596	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