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Detailed information for vg0617302802:

Variant ID: vg0617302802 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17302802
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAAACATGTAATAATTCAGAGCCTCGAACGACACCTAATCGAGTGTGGAGACCCAAGGAGGTAAAAGTTGAGAGACCGGTGGTTCCCCAGAGTAGTGAT[G/A]
AGTTCAATTTGATGAGAGAAGAATCATCGGTCATTAGAGAAGACTCTTCTCCACATGATGCTATCGGTGTTAATGTTGTATTCGTCTTGCCTTCGAAGTC

Reverse complement sequence

GACTTCGAAGGCAAGACGAATACAACATTAACACCGATAGCATCATGTGGAGAAGAGTCTTCTCTAATGACCGATGATTCTTCTCTCATCAAATTGAACT[C/T]
ATCACTACTCTGGGGAACCACCGGTCTCTCAACTTTTACCTCCTTGGGTCTCCACACTCGATTAGGTGTCGTTCGAGGCTCTGAATTATTACATGTTTCG

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	81.30%	17.30%	0.95%	0.40%	NA
All Indica	2759	99.10%	0.70%	0.18%	0.04%	NA
All Japonica	1512	44.30%	52.10%	2.38%	1.19%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	0.40%	0.51%	0.13%	NA
Temperate Japonica	767	9.30%	86.30%	2.09%	2.35%	NA
Tropical Japonica	504	92.50%	5.00%	2.58%	0.00%	NA
Japonica Intermediate	241	55.20%	41.90%	2.90%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	11.10%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0617302802	G -> A	LOC_Os06g30040.1	intron_variant ; MODIFIER	silent_mutation	Average:47.553; most accessible tissue: Zhenshan97 young leaf, score: 71.065	N	N	N	N
vg0617302802	G -> DEL	N	N	silent_mutation	Average:47.553; most accessible tissue: Zhenshan97 young leaf, score: 71.065	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617302802	NA	4.37E-23	mr1115	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
vg0617302802	NA	2.04E-31	mr1137	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
vg0617302802	NA	1.97E-11	mr1182	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
vg0617302802	NA	3.24E-07	mr1229	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
vg0617302802	NA	1.39E-06	mr1606	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
vg0617302802	NA	2.49E-12	mr1650	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
vg0617302802	NA	6.40E-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
vg0617302802	NA	1.48E-12	mr1667	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
vg0617302802	NA	3.65E-10	mr1552_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
vg0617302802	NA	2.40E-07	mr1578_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
vg0617302802	NA	2.53E-07	mr1582_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
vg0617302802	NA	1.07E-06	mr1695_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
vg0617302802	3.89E-06	NA	mr1761_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
vg0617302802	NA	1.05E-06	mr1761_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
vg0617302802	NA	6.62E-08	mr1952_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