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Detailed information for vg0619902184:

Variant ID: vg0619902184 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19902184
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTGAATTTTTTTTATAATTAATATTTTTATTTTTATTAGAGGATAAAGCTTGAATATTACGTTGTTGTGACTTTTTTTAATTTTTTTTTAAAAAAATT[C/T]
AAATAAGACAGATGGTCAAACGTTAAACACGGACACGCATAACTGCATGCACTTGAAATGGGATGGAGGCAGTATATGAGTAGCTCCAAAAACTGAGCCA

Reverse complement sequence

TGGCTCAGTTTTTGGAGCTACTCATATACTGCCTCCATCCCATTTCAAGTGCATGCAGTTATGCGTGTCCGTGTTTAACGTTTGACCATCTGTCTTATTT[G/A]
AATTTTTTTAAAAAAAAATTAAAAAAAGTCACAACAACGTAATATTCAAGCTTTATCCTCTAATAAAAATAAAAATATTAATTATAAAAAAAATTCAAAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.00%	20.40%	0.38%	0.30%	NA
All Indica	2759	98.90%	0.80%	0.18%	0.14%	NA
All Japonica	1512	41.00%	58.20%	0.79%	0.00%	NA
Aus	269	96.30%	0.00%	0.00%	3.72%	NA
Indica I	595	99.30%	0.50%	0.17%	0.00%	NA
Indica II	465	97.00%	2.60%	0.22%	0.22%	NA
Indica III	913	99.60%	0.10%	0.00%	0.33%	NA
Indica Intermediate	786	98.90%	0.80%	0.38%	0.00%	NA
Temperate Japonica	767	30.20%	69.20%	0.52%	0.00%	NA
Tropical Japonica	504	64.70%	34.30%	0.99%	0.00%	NA
Japonica Intermediate	241	25.70%	73.00%	1.24%	0.00%	NA
VI/Aromatic	96	65.60%	34.40%	0.00%	0.00%	NA
Intermediate	90	68.90%	30.00%	1.11%	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
vg0619902184	C -> T	LOC_Os06g34160.1	downstream_gene_variant ; 3750.0bp to feature; MODIFIER	silent_mutation	Average:56.35; most accessible tissue: Callus, score: 87.147	N	N	N	N
vg0619902184	C -> T	LOC_Os06g34180.1	downstream_gene_variant ; 2022.0bp to feature; MODIFIER	silent_mutation	Average:56.35; most accessible tissue: Callus, score: 87.147	N	N	N	N
vg0619902184	C -> T	LOC_Os06g34160-LOC_Os06g34180	intergenic_region ; MODIFIER	silent_mutation	Average:56.35; most accessible tissue: Callus, score: 87.147	N	N	N	N
vg0619902184	C -> DEL	N	N	silent_mutation	Average:56.35; most accessible tissue: Callus, score: 87.147	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619902184	NA	1.37E-09	mr1622	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
vg0619902184	NA	2.66E-08	mr1677	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
vg0619902184	NA	7.38E-07	mr1979	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