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Detailed information for vg0828161286:

Variant ID: vg0828161286 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 28161286
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGCACTGAAATTTTCTGTAACAGATATACATCTTAAAGGAAGAAGCAGCAACCTTTTCTACGATTGACAAAGCGCATGATTGTTTGTCCCATGATAAA[C/G]
TAACTCACAGAATACCAATTTACCTATTTTACTACATTGTCAGATTCCATATGCTCATGTACAGCAGCACAATGATTCATTTGATGCTCATATTCGGTTC

Reverse complement sequence

GAACCGAATATGAGCATCAAATGAATCATTGTGCTGCTGTACATGAGCATATGGAATCTGACAATGTAGTAAAATAGGTAAATTGGTATTCTGTGAGTTA[G/C]
TTTATCATGGGACAAACAATCATGCGCTTTGTCAATCGTAGAAAAGGTTGCTGCTTCTTCCTTTAAGATGTATATCTGTTACAGAAAATTTCAGTGCCTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.70%	11.70%	1.65%	0.00%	NA
All Indica	2759	99.70%	0.20%	0.14%	0.00%	NA
All Japonica	1512	59.60%	35.60%	4.76%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.70%	0.40%	0.86%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	28.00%	65.40%	6.52%	0.00%	NA
Tropical Japonica	504	95.00%	3.20%	1.79%	0.00%	NA
Japonica Intermediate	241	85.90%	8.70%	5.39%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	8.90%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0828161286	C -> G	LOC_Os08g44830.1	upstream_gene_variant ; 1957.0bp to feature; MODIFIER	silent_mutation	Average:45.685; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0828161286	C -> G	LOC_Os08g44840.1	downstream_gene_variant ; 1684.0bp to feature; MODIFIER	silent_mutation	Average:45.685; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0828161286	C -> G	LOC_Os08g44830-LOC_Os08g44840	intergenic_region ; MODIFIER	silent_mutation	Average:45.685; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0828161286	NA	2.71E-07	mr1648	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
vg0828161286	NA	2.10E-08	mr1806	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
vg0828161286	NA	4.69E-06	mr1398_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
vg0828161286	6.83E-06	NA	mr1484_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
vg0828161286	6.57E-06	4.56E-09	mr1659_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
vg0828161286	2.98E-06	2.98E-06	mr1659_2	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
vg0828161286	NA	3.43E-10	mr1806_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
vg0828161286	3.15E-08	NA	mr1829_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
vg0828161286	1.22E-07	NA	mr1902_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
vg0828161286	4.25E-06	NA	mr1945_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
vg0828161286	NA	8.79E-14	mr1959_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
vg0828161286	NA	8.45E-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
vg0828161286	7.34E-06	NA	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