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Detailed information for vg0402420137:

Variant ID: vg0402420137 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2420137
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAGTGCAACGAGGCCTGACATCTCATTTGCTGTGAGCAAGTTGAGCCGGTTTGTTTCAAATCCGGGAAATGATCATTGGCATGCTCTTGAAAGAGGAAT[G/A]
CGCTATCTAAAAGGGACAATGAGCTATGGAATTCACTACGCCGGGTACCCAAAAGTACTGGAGGGCTATAGTGATTCAACTAGATATCTGATGCTGATGA

Reverse complement sequence

TCATCAGCATCAGATATCTAGTTGAATCACTATAGCCCTCCAGTACTTTTGGGTACCCGGCGTAGTGAATTCCATAGCTCATTGTCCCTTTTAGATAGCG[C/T]
ATTCCTCTTTCAAGAGCATGCCAATGATCATTTCCCGGATTTGAAACAAACCGGCTCAACTTGCTCACAGCAAATGAGATGTCAGGCCTCGTTGCACTAG

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	34.80%	2.60%	27.32%	35.34%	NA
All Indica	2759	27.70%	0.00%	38.71%	33.53%	NA
All Japonica	1512	47.40%	7.10%	4.70%	40.87%	NA
Aus	269	42.00%	0.40%	33.09%	24.54%	NA
Indica I	595	19.70%	0.00%	47.23%	33.11%	NA
Indica II	465	23.40%	0.00%	37.63%	38.92%	NA
Indica III	913	32.30%	0.00%	33.30%	34.39%	NA
Indica Intermediate	786	31.00%	0.10%	39.19%	29.64%	NA
Temperate Japonica	767	83.20%	4.60%	1.43%	10.82%	NA
Tropical Japonica	504	4.20%	12.30%	9.72%	73.81%	NA
Japonica Intermediate	241	23.70%	4.10%	4.56%	67.63%	NA
VI/Aromatic	96	20.80%	7.30%	37.50%	34.38%	NA
Intermediate	90	33.30%	5.60%	30.00%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402420137	G -> DEL	N	N	silent_mutation	Average:7.399; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0402420137	G -> A	LOC_Os04g04999.1	upstream_gene_variant ; 3156.0bp to feature; MODIFIER	silent_mutation	Average:7.399; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0402420137	G -> A	LOC_Os04g04990.1	downstream_gene_variant ; 217.0bp to feature; MODIFIER	silent_mutation	Average:7.399; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0402420137	G -> A	LOC_Os04g04990-LOC_Os04g04999	intergenic_region ; MODIFIER	silent_mutation	Average:7.399; 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
vg0402420137	8.31E-07	4.66E-06	mr1457_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
vg0402420137	5.92E-06	NA	mr1543_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