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Detailed information for vg0620227512:

Variant ID: vg0620227512 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20227512
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTATTATGAAAAAATGTTTAAAAATAGATTTATCTCTGTTTTAATAGATAACGCCATTGATTTTGAACACACATTTGATCATTCATTTTATTAAAAAA[T/A]
TTACATAATTATAGTATATTTTATTGTGATTTGTTTTATCACTAATGTCGGTGACATGGGACCGGGAGTATCATGACTAGAGGTTTGGGCAGGAGCAATC

Reverse complement sequence

GATTGCTCCTGCCCAAACCTCTAGTCATGATACTCCCGGTCCCATGTCACCGACATTAGTGATAAAACAAATCACAATAAAATATACTATAATTATGTAA[A/T]
TTTTTTAATAAAATGAATGATCAAATGTGTGTTCAAAATCAATGGCGTTATCTATTAAAACAGAGATAAATCTATTTTTAAACATTTTTTCATAATAATT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.40%	7.50%	1.90%	1.21%	NA
All Indica	2759	98.00%	0.90%	1.05%	0.00%	NA
All Japonica	1512	71.40%	21.20%	3.64%	3.70%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.20%	0.50%	0.00%	NA
Indica II	465	96.60%	1.30%	2.15%	0.00%	NA
Indica III	913	97.90%	1.10%	0.99%	0.00%	NA
Indica Intermediate	786	98.10%	1.00%	0.89%	0.00%	NA
Temperate Japonica	767	88.70%	1.70%	3.00%	6.65%	NA
Tropical Japonica	504	35.70%	57.90%	5.75%	0.60%	NA
Japonica Intermediate	241	91.30%	6.60%	1.24%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	11.10%	6.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620227512	T -> A	LOC_Os06g34790.1	upstream_gene_variant ; 2717.0bp to feature; MODIFIER	silent_mutation	Average:30.257; most accessible tissue: Callus, score: 49.403	N	N	N	N
vg0620227512	T -> A	LOC_Os06g34800.1	downstream_gene_variant ; 1625.0bp to feature; MODIFIER	silent_mutation	Average:30.257; most accessible tissue: Callus, score: 49.403	N	N	N	N
vg0620227512	T -> A	LOC_Os06g34810.1	downstream_gene_variant ; 3255.0bp to feature; MODIFIER	silent_mutation	Average:30.257; most accessible tissue: Callus, score: 49.403	N	N	N	N
vg0620227512	T -> A	LOC_Os06g34800-LOC_Os06g34810	intergenic_region ; MODIFIER	silent_mutation	Average:30.257; most accessible tissue: Callus, score: 49.403	N	N	N	N
vg0620227512	T -> DEL	N	N	silent_mutation	Average:30.257; most accessible tissue: Callus, score: 49.403	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620227512	1.39E-06	NA	mr1334	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
vg0620227512	NA	5.28E-15	mr1334	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
vg0620227512	NA	7.12E-07	mr1250_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
vg0620227512	3.80E-07	NA	mr1334_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
vg0620227512	NA	8.21E-16	mr1334_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
vg0620227512	NA	3.30E-07	mr1786_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
vg0620227512	NA	2.06E-10	mr1991_2	Jap_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