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Detailed information for vg0606430642:

Variant ID: vg0606430642 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 6430642
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCTATTTAACCCTATCGGCTGTTTTCGATGATAGAGGCTAGCCGATGAGATTATATAGCTAGATCGATCCAGATTATATAGCATATATGATAACTCGGC[G/A]
GTTTACATAGATGGGGCTAGAGTGTCATGAAGATGCTAGCACTAGCCCCGAGAACGCAAGCCGCCATAACAAGCTTTACCTCTTCGTCGGAGATCGAAAC

Reverse complement sequence

GTTTCGATCTCCGACGAAGAGGTAAAGCTTGTTATGGCGGCTTGCGTTCTCGGGGCTAGTGCTAGCATCTTCATGACACTCTAGCCCCATCTATGTAAAC[C/T]
GCCGAGTTATCATATATGCTATATAATCTGGATCGATCTAGCTATATAATCTCATCGGCTAGCCTCTATCATCGAAAACAGCCGATAGGGTTAAATAGCC

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	91.30%	5.60%	1.48%	1.65%	NA
All Indica	2759	98.70%	0.50%	0.62%	0.14%	NA
All Japonica	1512	81.30%	15.30%	3.04%	0.33%	NA
Aus	269	98.50%	0.70%	0.37%	0.37%	NA
Indica I	595	98.70%	0.00%	1.34%	0.00%	NA
Indica II	465	99.60%	0.20%	0.00%	0.22%	NA
Indica III	913	99.60%	0.00%	0.33%	0.11%	NA
Indica Intermediate	786	97.30%	1.70%	0.76%	0.25%	NA
Temperate Japonica	767	94.90%	1.40%	3.65%	0.00%	NA
Tropical Japonica	504	57.10%	40.30%	2.58%	0.00%	NA
Japonica Intermediate	241	88.80%	7.10%	2.07%	2.07%	NA
VI/Aromatic	96	25.00%	5.20%	2.08%	67.71%	NA
Intermediate	90	80.00%	12.20%	4.44%	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
vg0606430642	G -> A	LOC_Os06g12010-LOC_Os06g12020	intergenic_region ; MODIFIER	silent_mutation	Average:30.864; most accessible tissue: Zhenshan97 young leaf, score: 50.0	N	N	N	N
vg0606430642	G -> DEL	N	N	silent_mutation	Average:30.864; most accessible tissue: Zhenshan97 young leaf, score: 50.0	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0606430642	NA	5.23E-07	mr1174_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
vg0606430642	1.41E-06	NA	mr1264_2	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
vg0606430642	NA	2.71E-08	mr1347_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
vg0606430642	NA	4.31E-06	mr1398_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
vg0606430642	NA	6.28E-11	mr1905_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