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Detailed information for vg0610636473:

Variant ID: vg0610636473 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10636473
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGATCGTCTTCGATCGCATGACGCTTGTATGTTCCTTGGAAATTGGCGACGAACTGCTGCCACAGGTCTGACCACGAAGAAATTGAGTAGGGGGGAGAT[A/G]
CATCAGCCACGAACGTGCAGAACCCTTCAACGCGGTTGGTAAATAGTTTGCCAACGCATTGTCATCTGCTCCAGCGGCATAAATGTAACATCCTGAAAAT

Reverse complement sequence

ATTTTCAGGATGTTACATTTATGCCGCTGGAGCAGATGACAATGCGTTGGCAAACTATTTACCAACCGCGTTGAAGGGTTCTGCACGTTCGTGGCTGATG[T/C]
ATCTCCCCCCTACTCAATTTCTTCGTGGTCAGACCTGTGGCAGCAGTTCGTCGCCAATTTCCAAGGAACATACAAGCGTCATGCGATCGAAGACGATCTT

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	39.60%	10.90%	15.83%	33.64%	NA
All Indica	2759	23.60%	5.00%	25.99%	45.38%	NA
All Japonica	1512	57.90%	24.30%	0.46%	17.33%	NA
Aus	269	83.60%	0.70%	4.09%	11.52%	NA
Indica I	595	17.00%	6.70%	27.39%	48.91%	NA
Indica II	465	12.70%	1.70%	31.40%	54.19%	NA
Indica III	913	30.70%	4.20%	23.55%	41.62%	NA
Indica Intermediate	786	27.00%	6.60%	24.55%	41.86%	NA
Temperate Japonica	767	44.30%	43.20%	0.52%	11.99%	NA
Tropical Japonica	504	70.00%	0.60%	0.60%	28.77%	NA
Japonica Intermediate	241	75.90%	13.70%	0.00%	10.37%	NA
VI/Aromatic	96	88.50%	0.00%	4.17%	7.29%	NA
Intermediate	90	37.80%	10.00%	10.00%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610636473	A -> G	LOC_Os06g18770.1	downstream_gene_variant ; 4850.0bp to feature; MODIFIER	silent_mutation	Average:15.48; most accessible tissue: Callus, score: 56.683	N	N	N	N
vg0610636473	A -> G	LOC_Os06g18750-LOC_Os06g18770	intergenic_region ; MODIFIER	silent_mutation	Average:15.48; most accessible tissue: Callus, score: 56.683	N	N	N	N
vg0610636473	A -> DEL	N	N	silent_mutation	Average:15.48; most accessible tissue: Callus, score: 56.683	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610636473	6.75E-06	NA	mr1027	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
vg0610636473	8.71E-12	NA	mr1087	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
vg0610636473	2.13E-07	9.62E-11	mr1087	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
vg0610636473	NA	2.82E-06	mr1096	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
vg0610636473	4.93E-08	NA	mr1087_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
vg0610636473	1.86E-08	1.97E-14	mr1087_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
vg0610636473	NA	3.03E-06	mr1091_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