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Detailed information for vg1008344509:

Variant ID: vg1008344509 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8344509
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.33, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGTCCTGTGTGCGTTCTTGGCGTATTGCTCTGCGAACTGTTTGTAGACGAAGCAATCTTTGGCCGCGTGGTTGGAGTTGGGATGATGCGGACATTGGG[A/G]
GTTCATGATCTTGTAAGTATTGACGCGGGAACGTTGTCGGGGGGATGGTGTAGTTGTCGCCACAAGTTCCTCGGGCTTATGCTTGCGATCCTTGTGATTG

Reverse complement sequence

CAATCACAAGGATCGCAAGCATAAGCCCGAGGAACTTGTGGCGACAACTACACCATCCCCCCGACAACGTTCCCGCGTCAATACTTACAAGATCATGAAC[T/C]
CCCAATGTCCGCATCATCCCAACTCCAACCACGCGGCCAAAGATTGCTTCGTCTACAAACAGTTCGCAGAGCAATACGCCAAGAACGCACACAGGACTTC

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	61.10%	21.20%	0.42%	17.27%	NA
All Indica	2759	73.70%	2.90%	0.65%	22.73%	NA
All Japonica	1512	29.50%	58.70%	0.13%	11.71%	NA
Aus	269	98.90%	0.40%	0.00%	0.74%	NA
Indica I	595	96.60%	0.20%	1.18%	2.02%	NA
Indica II	465	77.80%	0.60%	0.43%	21.08%	NA
Indica III	913	53.90%	6.20%	0.88%	38.99%	NA
Indica Intermediate	786	76.80%	2.50%	0.13%	20.48%	NA
Temperate Japonica	767	7.80%	87.90%	0.00%	4.30%	NA
Tropical Japonica	504	68.50%	14.30%	0.20%	17.06%	NA
Japonica Intermediate	241	17.00%	58.50%	0.41%	24.07%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	67.80%	21.10%	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
vg1008344509	A -> G	LOC_Os10g16750.1	missense_variant ; p.Ser468Pro; MODERATE	nonsynonymous_codon ; S468P	Average:28.397; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	benign	0.499	DELETERIOUS	0.01
vg1008344509	A -> DEL	LOC_Os10g16750.1	N	frameshift_variant	Average:28.397; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1008344509	NA	1.02E-06	Awn_length	Ind_All	Not	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
vg1008344509	NA	2.06E-07	mr1113	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
vg1008344509	NA	1.17E-06	mr1120	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
vg1008344509	4.33E-06	4.33E-06	mr1355	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
vg1008344509	NA	5.48E-06	mr1619	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
vg1008344509	NA	3.16E-06	mr1642	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
vg1008344509	NA	7.10E-09	mr1693	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
vg1008344509	NA	4.32E-06	mr1842	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
vg1008344509	NA	3.85E-08	mr1864	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
vg1008344509	NA	9.73E-06	mr1114_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
vg1008344509	NA	6.92E-07	mr1120_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
vg1008344509	NA	3.06E-06	mr1258_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
vg1008344509	NA	4.19E-14	mr1790_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
vg1008344509	NA	7.42E-07	mr1991_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