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Detailed information for vg0610862201:

Variant ID: vg0610862201 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10862201
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTAGAGAGAAACTATACGTAAGGGGACGCTGGCCGGTATGTCAGCATTTATTCGGTACGTACATCACGATTGTCACTTCTTACTTCTGACGTGTCCACT[T/G]
ATGTATGCAGTGTTATAAGCAACCTAGCTTGACGAACCTATGTGATTATTGCGTGTGCGAGATGCCCAGGGTCAGTGGGAGATACGAAACTGAGTTTACA

Reverse complement sequence

TGTAAACTCAGTTTCGTATCTCCCACTGACCCTGGGCATCTCGCACACGCAATAATCACATAGGTTCGTCAAGCTAGGTTGCTTATAACACTGCATACAT[A/C]
AGTGGACACGTCAGAAGTAAGAAGTGACAATCGTGATGTACGTACCGAATAAATGCTGACATACCGGCCAGCGTCCCCTTACGTATAGTTTCTCTCTACT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.70%	4.20%	32.69%	0.38%	NA
All Indica	2759	38.60%	6.80%	54.48%	0.07%	NA
All Japonica	1512	98.00%	0.20%	0.73%	1.06%	NA
Aus	269	98.10%	0.00%	1.86%	0.00%	NA
Indica I	595	29.20%	6.40%	64.20%	0.17%	NA
Indica II	465	31.20%	12.30%	56.34%	0.22%	NA
Indica III	913	43.30%	5.10%	51.59%	0.00%	NA
Indica Intermediate	786	44.80%	5.90%	49.36%	0.00%	NA
Temperate Japonica	767	97.40%	0.30%	0.91%	1.43%	NA
Tropical Japonica	504	99.20%	0.20%	0.20%	0.40%	NA
Japonica Intermediate	241	97.50%	0.00%	1.24%	1.24%	NA
VI/Aromatic	96	94.80%	0.00%	5.21%	0.00%	NA
Intermediate	90	68.90%	7.80%	23.33%	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
vg0610862201	T -> G	LOC_Os06g19095.1	downstream_gene_variant ; 3194.0bp to feature; MODIFIER	silent_mutation	Average:13.82; most accessible tissue: Callus, score: 22.504	N	N	N	N
vg0610862201	T -> G	LOC_Os06g19090.1	intron_variant ; MODIFIER	silent_mutation	Average:13.82; most accessible tissue: Callus, score: 22.504	N	N	N	N
vg0610862201	T -> DEL	N	N	silent_mutation	Average:13.82; most accessible tissue: Callus, score: 22.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610862201	2.83E-06	NA	mr1056	Ind_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
vg0610862201	6.76E-06	NA	mr1478	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
vg0610862201	7.24E-06	NA	mr1478	Ind_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