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Detailed information for vg0300327473:

Variant ID: vg0300327473 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 327473
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAATCAAATCGATGAAAACTCATTCAAGATGGTAGATACACCGCATAGTCTAGCTTGATATCGAAGCCTAAACCTGCCTCTCGATGATAGAGGCTAGCC[G/A]
ATGAAGTTTAGATGACGAAACCAATCTAGACTATGCGGTATATATGATAACTCGGCGGTTTACATAGACAGGATTAGAGTGTCATGAAGATGCAAGCACT

Reverse complement sequence

AGTGCTTGCATCTTCATGACACTCTAATCCTGTCTATGTAAACCGCCGAGTTATCATATATACCGCATAGTCTAGATTGGTTTCGTCATCTAAACTTCAT[C/T]
GGCTAGCCTCTATCATCGAGAGGCAGGTTTAGGCTTCGATATCAAGCTAGACTATGCGGTGTATCTACCATCTTGAATGAGTTTTCATCGATTTGATTAG

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	52.10%	0.80%	11.51%	35.55%	NA
All Indica	2759	23.80%	1.10%	19.03%	56.03%	NA
All Japonica	1512	99.70%	0.00%	0.00%	0.26%	NA
Aus	269	50.60%	2.20%	6.32%	40.89%	NA
Indica I	595	13.10%	1.00%	17.98%	67.90%	NA
Indica II	465	43.20%	0.20%	8.60%	47.96%	NA
Indica III	913	16.80%	2.20%	26.73%	54.33%	NA
Indica Intermediate	786	28.80%	0.40%	17.05%	53.82%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	75.60%	1.10%	1.11%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0300327473	G -> A	LOC_Os03g01500.1	upstream_gene_variant ; 1491.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0300327473	G -> A	LOC_Os03g01490.1	downstream_gene_variant ; 3830.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0300327473	G -> A	LOC_Os03g01500-LOC_Os03g01520	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0300327473	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0300327473	4.17E-06	NA	mr1944	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
vg0300327473	NA	1.98E-08	mr1944	Ind_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