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Detailed information for vg0819413870:

Variant ID: vg0819413870 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19413870
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCACTTTTCTTTCGCTTGTATCGAGATGCCTTGCAGACAGGACAAGCATCCAAGTCCGCATATTGCTTGTGGTACAATATGCAGTCGTTTGGACAAGC[G/A]
TGAATTCTACGGACCTCTAACCCCAGTGGACATAGAACCTGCTTTGCTTCGTATGTCGTCTCGGGCAATGTGTTCTCATCAGGAAGCATAGCCTTCAAAA

Reverse complement sequence

TTTTGAAGGCTATGCTTCCTGATGAGAACACATTGCCCGAGACGACATACGAAGCAAAGCAGGTTCTATGTCCACTGGGGTTAGAGGTCCGTAGAATTCA[C/T]
GCTTGTCCAAACGACTGCATATTGTACCACAAGCAATATGCGGACTTGGATGCTTGTCCTGTCTGCAAGGCATCTCGATACAAGCGAAAGAAAAGTGCTG

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	40.00%	7.10%	51.10%	1.78%	NA
All Indica	2759	10.80%	10.90%	75.53%	2.75%	NA
All Japonica	1512	82.20%	1.80%	15.67%	0.33%	NA
Aus	269	78.10%	1.10%	20.82%	0.00%	NA
Indica I	595	4.70%	8.90%	81.18%	5.21%	NA
Indica II	465	5.40%	9.90%	81.51%	3.23%	NA
Indica III	913	17.00%	12.70%	69.77%	0.55%	NA
Indica Intermediate	786	11.50%	10.90%	74.43%	3.18%	NA
Temperate Japonica	767	99.30%	0.10%	0.39%	0.13%	NA
Tropical Japonica	504	53.60%	5.00%	40.67%	0.79%	NA
Japonica Intermediate	241	87.60%	0.40%	12.03%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	52.20%	3.30%	41.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0819413870	G -> A	LOC_Os08g31400.1	synonymous_variant ; p.His220His; LOW	synonymous_codon	Average:15.429; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0819413870	G -> DEL	LOC_Os08g31400.1	N	frameshift_variant	Average:15.429; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819413870	NA	3.34E-06	mr1227_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
vg0819413870	NA	7.23E-06	mr1407_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
vg0819413870	2.29E-06	2.29E-06	mr1464_2	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
vg0819413870	7.82E-06	3.17E-06	mr1541_2	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
vg0819413870	NA	7.47E-06	mr1735_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
vg0819413870	NA	6.65E-06	mr1759_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
vg0819413870	NA	3.93E-06	mr1869_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
vg0819413870	8.05E-06	8.05E-06	mr1869_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