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Detailed information for vg0619254766:

Variant ID: vg0619254766 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19254766
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGATGTTATCCGATCCATATCTAATAAAAAACCTTTACACGTTCCAATATTAAATTCAAACTTTCACATATGCAAGGCGCAGCATAGTGTGTCCTACT[A/G]
GCGAGAGTCCACCCAACTTTCGCTCCTGAAGTCGCTGAGGGCATGGATTTCAAGCCCTCGGTTACAGACAAGGTCCACGGCGCAGACCTGCTAGCTGGGT

Reverse complement sequence

ACCCAGCTAGCAGGTCTGCGCCGTGGACCTTGTCTGTAACCGAGGGCTTGAAATCCATGCCCTCAGCGACTTCAGGAGCGAAAGTTGGGTGGACTCTCGC[T/C]
AGTAGGACACACTATGCTGCGCCTTGCATATGTGAAAGTTTGAATTTAATATTGGAACGTGTAAAGGTTTTTTATTAGATATGGATCGGATAACATCAAT

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	65.50%	28.30%	0.13%	6.12%	NA
All Indica	2759	93.40%	6.20%	0.04%	0.40%	NA
All Japonica	1512	6.50%	75.10%	0.26%	18.19%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.30%	6.40%	0.00%	1.34%	NA
Indica II	465	93.80%	6.20%	0.00%	0.00%	NA
Indica III	913	97.60%	2.30%	0.11%	0.00%	NA
Indica Intermediate	786	89.10%	10.60%	0.00%	0.38%	NA
Temperate Japonica	767	3.70%	68.70%	0.52%	27.12%	NA
Tropical Japonica	504	11.70%	84.90%	0.00%	3.37%	NA
Japonica Intermediate	241	4.60%	74.70%	0.00%	20.75%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	63.30%	33.30%	0.00%	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
vg0619254766	A -> G	LOC_Os06g33070.1	synonymous_variant ; p.Leu420Leu; LOW	synonymous_codon	Average:47.271; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0619254766	A -> DEL	LOC_Os06g33070.1	N	frameshift_variant	Average:47.271; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619254766	NA	2.79E-06	mr1111	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
vg0619254766	NA	1.13E-07	mr1354	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
vg0619254766	NA	7.61E-07	mr1528	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
vg0619254766	NA	7.46E-13	mr1900	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
vg0619254766	NA	8.07E-07	mr1111_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
vg0619254766	NA	1.32E-06	mr1144_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
vg0619254766	NA	2.14E-06	mr1369_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
vg0619254766	NA	4.71E-07	mr1453_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
vg0619254766	NA	1.01E-07	mr1681_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