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Detailed information for vg0206101296:

Variant ID: vg0206101296 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6101296
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCTAGAAAACTTAGCCCCCACACTTGGCGAGGAAACGTTCATGTAGATGAGAAAGAGGTTGGGCTCTTACCACCGAGGAAGCAAACGAATGCGCAATAC[A/G]
CGAGCGTCACAGGGCCATGAGAAAAGAATGGGGGAAAAGAAATATAAGACTTCAAGCTGTATTAAGCTGATGAATTGAAAAATTGAAAATACTTGAAGGT

Reverse complement sequence

ACCTTCAAGTATTTTCAATTTTTCAATTCATCAGCTTAATACAGCTTGAAGTCTTATATTTCTTTTCCCCCATTCTTTTCTCATGGCCCTGTGACGCTCG[T/C]
GTATTGCGCATTCGTTTGCTTCCTCGGTGGTAAGAGCCCAACCTCTTTCTCATCTACATGAACGTTTCCTCGCCAAGTGTGGGGGCTAAGTTTTCTAGCC

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	38.70%	31.30%	0.83%	29.24%	NA
All Indica	2759	51.60%	1.10%	1.41%	45.89%	NA
All Japonica	1512	2.90%	91.90%	0.00%	5.16%	NA
Aus	269	98.90%	0.70%	0.00%	0.37%	NA
Indica I	595	56.50%	0.70%	1.51%	41.34%	NA
Indica II	465	62.80%	0.60%	0.65%	35.91%	NA
Indica III	913	42.60%	1.00%	1.64%	54.76%	NA
Indica Intermediate	786	51.90%	1.70%	1.53%	44.91%	NA
Temperate Japonica	767	1.80%	89.00%	0.00%	9.13%	NA
Tropical Japonica	504	4.00%	95.40%	0.00%	0.60%	NA
Japonica Intermediate	241	4.10%	93.80%	0.00%	2.07%	NA
VI/Aromatic	96	56.20%	19.80%	0.00%	23.96%	NA
Intermediate	90	43.30%	41.10%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0206101296	A -> G	LOC_Os02g11800.1	downstream_gene_variant ; 3367.0bp to feature; MODIFIER	silent_mutation	Average:26.144; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0206101296	A -> G	LOC_Os02g11790-LOC_Os02g11800	intergenic_region ; MODIFIER	silent_mutation	Average:26.144; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0206101296	A -> DEL	N	N	silent_mutation	Average:26.144; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206101296	NA	3.92E-06	mr1291	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
vg0206101296	NA	9.07E-23	mr1383	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
vg0206101296	NA	1.27E-19	mr1557	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
vg0206101296	NA	8.89E-14	mr1641	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
vg0206101296	NA	3.49E-06	mr1646	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
vg0206101296	NA	9.71E-17	mr1653	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
vg0206101296	NA	7.05E-21	mr1715	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
vg0206101296	NA	9.87E-07	mr1815	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
vg0206101296	NA	2.03E-34	mr1944	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
vg0206101296	NA	4.52E-07	mr1358_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
vg0206101296	NA	7.46E-10	mr1379_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
vg0206101296	NA	3.56E-06	mr1559_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
vg0206101296	NA	3.21E-09	mr1576_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
vg0206101296	NA	1.17E-08	mr1749_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
vg0206101296	NA	8.66E-09	mr1821_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