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Detailed information for vg0721449575:

Variant ID: vg0721449575 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21449575
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.78, G: 0.22, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAATGAAACAACTATTTTCAACTGGGGCGGATGTAGGATTTGGGTGGTGTCTGGAAAAGGCTAGTGCCGTCCCTGGTCAGTTAAGGACCGAGCCATGA[G/A]
GTTAAGCATGAAACGACCCCCGTACAACCACACTTCTCGTATGGGTATAGACCTAGCGGAGTAGATAGATGAGCGGAGGCAGTATCCATGCATAGTGGTT

Reverse complement sequence

AACCACTATGCATGGATACTGCCTCCGCTCATCTATCTACTCCGCTAGGTCTATACCCATACGAGAAGTGTGGTTGTACGGGGGTCGTTTCATGCTTAAC[C/T]
TCATGGCTCGGTCCTTAACTGACCAGGGACGGCACTAGCCTTTTCCAGACACCACCCAAATCCTACATCCGCCCCAGTTGAAAATAGTTGTTTCATTTTA

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	54.40%	27.00%	3.72%	14.92%	NA
All Indica	2759	60.70%	11.90%	4.20%	23.27%	NA
All Japonica	1512	49.00%	45.50%	2.71%	2.78%	NA
Aus	269	27.10%	62.10%	5.58%	5.20%	NA
Indica I	595	82.40%	3.50%	1.01%	13.11%	NA
Indica II	465	38.50%	9.20%	2.80%	49.46%	NA
Indica III	913	55.40%	20.40%	7.01%	17.20%	NA
Indica Intermediate	786	63.50%	9.80%	4.20%	22.52%	NA
Temperate Japonica	767	26.70%	62.70%	5.35%	5.22%	NA
Tropical Japonica	504	73.80%	26.20%	0.00%	0.00%	NA
Japonica Intermediate	241	68.00%	31.10%	0.00%	0.83%	NA
VI/Aromatic	96	39.60%	59.40%	1.04%	0.00%	NA
Intermediate	90	50.00%	38.90%	3.33%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0721449575	G -> DEL	N	N	silent_mutation	Average:28.441; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg0721449575	G -> A	LOC_Os07g35810.1	upstream_gene_variant ; 4752.0bp to feature; MODIFIER	silent_mutation	Average:28.441; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg0721449575	G -> A	LOC_Os07g35820.1	upstream_gene_variant ; 1132.0bp to feature; MODIFIER	silent_mutation	Average:28.441; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg0721449575	G -> A	LOC_Os07g35820-LOC_Os07g35840	intergenic_region ; MODIFIER	silent_mutation	Average:28.441; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721449575	NA	2.87E-07	mr1330	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
vg0721449575	NA	5.68E-07	mr1627	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
vg0721449575	NA	1.08E-08	mr1770	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
vg0721449575	2.54E-06	2.54E-06	mr1779	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
vg0721449575	NA	9.92E-07	mr1805	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
vg0721449575	NA	2.06E-06	mr1910	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
vg0721449575	NA	5.15E-09	mr1946	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
vg0721449575	NA	5.28E-06	mr1977	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
vg0721449575	NA	7.18E-07	mr1977	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
vg0721449575	NA	4.96E-10	mr1364_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
vg0721449575	NA	1.58E-13	mr1807_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
vg0721449575	NA	4.20E-06	mr1959_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