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Detailed information for vg1004372176:

Variant ID: vg1004372176 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4372176
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

ACGCGCAGCTGCAAGCTCAGCCGGTCGCTGCCCAAGCACACTCTCAGCCGCCTGGCCAAGTGTTACAAGCAATGGCAGAAGGGGCTTCGGCTCTGCAAGC[G/A]
CAACTTCAAGCTCTCCTTCAACAACTTAGGCCCTGTTTCTTTCAGCTTGGGATTATTATAATCAGATTATTGGGAGTAAGCTGAAAGAAACAGACAACTT

Reverse complement sequence

AAGTTGTCTGTTTCTTTCAGCTTACTCCCAATAATCTGATTATAATAATCCCAAGCTGAAAGAAACAGGGCCTAAGTTGTTGAAGGAGAGCTTGAAGTTG[C/T]
GCTTGCAGAGCCGAAGCCCCTTCTGCCATTGCTTGTAACACTTGGCCAGGCGGCTGAGAGTGTGCTTGGGCAGCGACCGGCTGAGCTTGCAGCTGCGCGT

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	30.10%	16.20%	2.39%	51.35%	NA
All Indica	2759	22.00%	16.50%	1.45%	60.09%	NA
All Japonica	1512	50.50%	1.40%	4.56%	43.52%	NA
Aus	269	1.10%	93.30%	0.74%	4.83%	NA
Indica I	595	32.30%	42.40%	2.86%	22.52%	NA
Indica II	465	21.10%	10.80%	0.65%	67.53%	NA
Indica III	913	11.60%	3.40%	0.88%	84.12%	NA
Indica Intermediate	786	26.70%	15.50%	1.53%	56.23%	NA
Temperate Japonica	767	76.00%	0.30%	6.52%	17.21%	NA
Tropical Japonica	504	16.90%	2.20%	2.18%	78.77%	NA
Japonica Intermediate	241	39.80%	3.30%	3.32%	53.53%	NA
VI/Aromatic	96	16.70%	20.80%	0.00%	62.50%	NA
Intermediate	90	36.70%	18.90%	2.22%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004372176	G -> A	LOC_Os10g08070.1	missense_variant ; p.Ala218Thr; MODERATE	nonsynonymous_codon ; A218T	Average:46.834; most accessible tissue: Zhenshan97 flag leaf, score: 80.373	unknown	unknown	TOLERATED	0.06
vg1004372176	G -> DEL	LOC_Os10g08070.1	N	frameshift_variant	Average:46.834; most accessible tissue: Zhenshan97 flag leaf, score: 80.373	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004372176	NA	9.59E-08	mr1087	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
vg1004372176	NA	4.54E-07	mr1090	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
vg1004372176	NA	5.96E-06	mr1094	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
vg1004372176	NA	1.17E-06	mr1096	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
vg1004372176	3.49E-06	3.49E-06	mr1234	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
vg1004372176	NA	4.85E-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
vg1004372176	NA	3.43E-09	mr1658	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
vg1004372176	NA	1.33E-06	mr1608_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