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Detailed information for vg0421211457:

Variant ID: vg0421211457 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21211457
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCTCCGGAAGCGGGCGGCAATGGCGGCGAGGCCATGCCGAGCGGCGGCGGAGCTCGGGGCGGTGTCTACGCGCTTTCGAGGGGCTAGTAGAGCTACCAC[G/A]
CAAGCTAGAGAGGGCGAGGGAGAACGAGGAAGGAGAATGGAGGGAGTCACTACCGAGTCGGGACGGCACCGTGACGAGTGGCCGACGGTGCGGGAGTGAG

Reverse complement sequence

CTCACTCCCGCACCGTCGGCCACTCGTCACGGTGCCGTCCCGACTCGGTAGTGACTCCCTCCATTCTCCTTCCTCGTTCTCCCTCGCCCTCTCTAGCTTG[C/T]
GTGGTAGCTCTACTAGCCCCTCGAAAGCGCGTAGACACCGCCCCGAGCTCCGCCGCCGCTCGGCATGGCCTCGCCGCCATTGCCGCCCGCTTCCGGAGGC

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	88.60%	5.00%	0.95%	5.52%	NA
All Indica	2759	90.10%	0.30%	0.72%	8.92%	NA
All Japonica	1512	84.10%	14.70%	1.12%	0.13%	NA
Aus	269	97.40%	0.00%	1.86%	0.74%	NA
Indica I	595	84.00%	0.00%	1.68%	14.29%	NA
Indica II	465	78.70%	0.60%	0.86%	19.78%	NA
Indica III	913	98.10%	0.00%	0.00%	1.86%	NA
Indica Intermediate	786	92.00%	0.60%	0.76%	6.62%	NA
Temperate Japonica	767	98.20%	1.70%	0.13%	0.00%	NA
Tropical Japonica	504	57.50%	39.50%	2.78%	0.20%	NA
Japonica Intermediate	241	94.60%	4.10%	0.83%	0.41%	NA
VI/Aromatic	96	88.50%	0.00%	1.04%	10.42%	NA
Intermediate	90	92.20%	4.40%	2.22%	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
vg0421211457	G -> DEL	N	N	silent_mutation	Average:22.276; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0421211457	G -> A	LOC_Os04g34910.1	upstream_gene_variant ; 3487.0bp to feature; MODIFIER	silent_mutation	Average:22.276; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0421211457	G -> A	LOC_Os04g34900.1	downstream_gene_variant ; 3172.0bp to feature; MODIFIER	silent_mutation	Average:22.276; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0421211457	G -> A	LOC_Os04g34900-LOC_Os04g34910	intergenic_region ; MODIFIER	silent_mutation	Average:22.276; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421211457	1.37E-06	3.95E-07	mr1177	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