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Detailed information for vg0807470228:

Variant ID: vg0807470228 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7470228
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCGCCTGACATCCTGGGTCCCATCAGTCATTCGACCGGTCACAGACCGGTTGAGTGCACTGCACACTGCATTAAATGCGGTGTGGCGCGACCGCTTGG[A/G]
TTGCCATAAATGCGGGTAGGTGGGCACCTGGAGGCGGACACCTAACCCACCGTACGTGGAGACATAGAGAGGGGGTCGGCGGAGCCCGACCCCTAGTCAC

Reverse complement sequence

GTGACTAGGGGTCGGGCTCCGCCGACCCCCTCTCTATGTCTCCACGTACGGTGGGTTAGGTGTCCGCCTCCAGGTGCCCACCTACCCGCATTTATGGCAA[T/C]
CCAAGCGGTCGCGCCACACCGCATTTAATGCAGTGTGCAGTGCACTCAACCGGTCTGTGACCGGTCGAATGACTGATGGGACCCAGGATGTCAGGCGCAC

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	33.90%	21.40%	15.57%	29.16%	NA
All Indica	2759	3.90%	25.10%	22.62%	48.39%	NA
All Japonica	1512	96.00%	1.60%	1.12%	1.26%	NA
Aus	269	0.70%	75.80%	22.30%	1.12%	NA
Indica I	595	7.40%	11.10%	6.05%	75.46%	NA
Indica II	465	4.50%	43.90%	12.47%	39.14%	NA
Indica III	913	1.40%	21.00%	41.29%	36.25%	NA
Indica Intermediate	786	3.70%	29.40%	19.47%	47.46%	NA
Temperate Japonica	767	95.80%	0.50%	1.56%	2.09%	NA
Tropical Japonica	504	96.20%	2.80%	0.79%	0.20%	NA
Japonica Intermediate	241	96.30%	2.50%	0.41%	0.83%	NA
VI/Aromatic	96	4.20%	72.90%	22.92%	0.00%	NA
Intermediate	90	40.00%	22.20%	14.44%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0807470228	A -> G	LOC_Os08g12630.1	downstream_gene_variant ; 497.0bp to feature; MODIFIER	silent_mutation	Average:52.638; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0807470228	A -> G	LOC_Os08g12620-LOC_Os08g12630	intergenic_region ; MODIFIER	silent_mutation	Average:52.638; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0807470228	A -> DEL	N	N	silent_mutation	Average:52.638; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807470228	NA	1.06E-44	mr1136	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
vg0807470228	NA	2.22E-08	mr1162	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
vg0807470228	NA	1.96E-47	mr1194	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
vg0807470228	NA	3.69E-23	mr1383	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
vg0807470228	NA	4.21E-36	mr1402	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
vg0807470228	2.03E-08	2.27E-09	mr1415	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
vg0807470228	NA	3.17E-41	mr1480	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
vg0807470228	NA	6.38E-18	mr1529	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
vg0807470228	2.03E-08	2.27E-09	mr1567	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
vg0807470228	NA	4.15E-06	mr1577	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
vg0807470228	NA	1.74E-23	mr1588	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
vg0807470228	6.02E-06	4.29E-07	mr1588	Ind_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
vg0807470228	NA	1.49E-08	mr1637	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
vg0807470228	NA	1.73E-14	mr1641	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
vg0807470228	NA	1.97E-53	mr1692	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
vg0807470228	NA	3.28E-18	mr1715	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
vg0807470228	NA	2.42E-06	mr1761	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
vg0807470228	NA	2.27E-34	mr1780	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
vg0807470228	NA	5.91E-08	mr1815	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
vg0807470228	NA	3.96E-22	mr1839	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
vg0807470228	NA	5.34E-14	mr1909	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
vg0807470228	NA	3.88E-10	mr1921	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
vg0807470228	NA	2.31E-15	mr1162_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
vg0807470228	NA	1.65E-07	mr1334_2	Ind_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
vg0807470228	NA	1.02E-18	mr1383_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
vg0807470228	NA	3.56E-35	mr1448_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
vg0807470228	NA	3.79E-53	mr1480_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
vg0807470228	6.72E-06	NA	mr1567_2	Ind_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
vg0807470228	NA	7.64E-12	mr1636_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
vg0807470228	NA	2.34E-13	mr1641_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
vg0807470228	NA	2.13E-24	mr1653_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
vg0807470228	NA	3.14E-18	mr1682_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
vg0807470228	NA	2.93E-08	mr1683_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
vg0807470228	NA	2.25E-16	mr1715_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
vg0807470228	NA	1.12E-34	mr1780_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
vg0807470228	8.48E-07	1.82E-06	mr1806_2	Ind_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
vg0807470228	NA	8.54E-15	mr1838_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
vg0807470228	NA	4.56E-22	mr1968_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