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Detailed information for vg0406860650:

Variant ID: vg0406860650 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6860650
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.55, G: 0.45, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAACTCTGTCGCCCTATCCACCGCCGAAGCGGAATATGTTTCGGCGGGGAGTTGTTGTGCTCAACTTCTTTGGATGAAGCAAACCCTGAGAGACTATG[A/G]
CCTCAATGTATCTACAATCCCACTCCTATGTGACAATGAGTGCGCCACTAAGATAGCCAACAACCCCGTCCAACACTCCCGAACCAAACATATCGATATT

Reverse complement sequence

AATATCGATATGTTTGGTTCGGGAGTGTTGGACGGGGTTGTTGGCTATCTTAGTGGCGCACTCATTGTCACATAGGAGTGGGATTGTAGATACATTGAGG[T/C]
CATAGTCTCTCAGGGTTTGCTTCATCCAAAGAAGTTGAGCACAACAACTCCCCGCCGAAACATATTCCGCTTCGGCGGTGGATAGGGCGACAGAGTTTTG

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	44.40%	43.70%	0.42%	11.45%	NA
All Indica	2759	21.10%	62.70%	0.62%	15.55%	NA
All Japonica	1512	95.40%	4.00%	0.07%	0.46%	NA
Aus	269	0.70%	72.50%	0.37%	26.39%	NA
Indica I	595	7.90%	75.30%	1.34%	15.46%	NA
Indica II	465	21.30%	64.30%	0.65%	13.76%	NA
Indica III	913	25.60%	57.80%	0.33%	16.21%	NA
Indica Intermediate	786	25.70%	58.00%	0.38%	15.90%	NA
Temperate Japonica	767	96.90%	3.00%	0.00%	0.13%	NA
Tropical Japonica	504	95.80%	3.60%	0.20%	0.40%	NA
Japonica Intermediate	241	90.00%	8.30%	0.00%	1.66%	NA
VI/Aromatic	96	20.80%	52.10%	0.00%	27.08%	NA
Intermediate	90	56.70%	33.30%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406860650	A -> DEL	N	N	silent_mutation	Average:27.423; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg0406860650	A -> G	LOC_Os04g12420.1	intron_variant ; MODIFIER	silent_mutation	Average:27.423; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406860650	NA	5.19E-14	mr1035	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
vg0406860650	NA	1.21E-11	mr1233	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
vg0406860650	NA	3.83E-08	mr1233	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
vg0406860650	5.74E-06	5.74E-06	mr1353	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
vg0406860650	9.50E-06	NA	mr1395	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
vg0406860650	5.60E-06	NA	mr1618	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
vg0406860650	NA	1.13E-12	mr1626	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
vg0406860650	NA	4.31E-06	mr1730	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
vg0406860650	2.71E-06	2.71E-06	mr1866	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
vg0406860650	NA	3.92E-19	mr1913	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
vg0406860650	NA	3.10E-11	mr1949	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
vg0406860650	NA	1.28E-06	mr1949	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
vg0406860650	NA	1.40E-07	mr1212_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