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Detailed information for vg0221672389:

Variant ID: vg0221672389 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21672389
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTTGCACCACCAATTCCGAATCACCAAAGTCCTCCACATATTTAGCTCCAACCATCTCCATAACTTGTAAGCCGAACAATAAAGCATTGTATTCGGCTT[A/G]
ATTATTTGTGCAATAATATTCTAAACGAACCGATGCCTCGTAACACATGCCATTAGGTGAAAACAAAACTACCCCTATGCTTTGTCCTTCTTTGCAAGAA

Reverse complement sequence

TTCTTGCAAAGAAGGACAAAGCATAGGGGTAGTTTTGTTTTCACCTAATGGCATGTGTTACGAGGCATCGGTTCGTTTAGAATATTATTGCACAAATAAT[T/C]
AAGCCGAATACAATGCTTTATTGTTCGGCTTACAAGTTATGGAGATGGTTGGAGCTAAATATGTGGAGGACTTTGGTGATTCGGAATTGGTGGTGCAACA

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	60.00%	35.50%	3.17%	1.29%	NA
All Indica	2759	89.70%	4.30%	4.78%	1.23%	NA
All Japonica	1512	3.90%	93.90%	0.73%	1.46%	NA
Aus	269	97.00%	1.10%	1.86%	0.00%	NA
Indica I	595	85.90%	5.20%	7.06%	1.85%	NA
Indica II	465	86.70%	2.60%	7.96%	2.80%	NA
Indica III	913	95.70%	2.20%	1.97%	0.11%	NA
Indica Intermediate	786	87.40%	7.00%	4.45%	1.15%	NA
Temperate Japonica	767	1.20%	98.70%	0.13%	0.00%	NA
Tropical Japonica	504	8.10%	86.30%	1.98%	3.57%	NA
Japonica Intermediate	241	3.70%	94.60%	0.00%	1.66%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	34.40%	57.80%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0221672389	A -> G	LOC_Os02g36040.1	downstream_gene_variant ; 4593.0bp to feature; MODIFIER	silent_mutation	Average:12.72; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0221672389	A -> G	LOC_Os02g36060.1	downstream_gene_variant ; 3954.0bp to feature; MODIFIER	silent_mutation	Average:12.72; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0221672389	A -> G	LOC_Os02g36050.1	intron_variant ; MODIFIER	silent_mutation	Average:12.72; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0221672389	A -> DEL	N	N	silent_mutation	Average:12.72; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221672389	NA	6.24E-06	mr1623	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
vg0221672389	NA	1.95E-06	mr1691_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