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Detailed information for vg0322412591:

Variant ID: vg0322412591 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22412591
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCACAACATAGAATCCTACATACGCCAAGACACGCCGCCGGATATCGACTTCAGGGATAAGCACGGCTAGTACCCTACGGTGTCTCCGGATACTGTCAG[G/A]
AGAGACGAAAGCGCTATCTCTGATCTCGCCGGGCACGGATTCGAGGAGGAAGGCTACCCTGTTGTCGACTACGAGTCAGATCGTCAGACCGCCATGTCGA

Reverse complement sequence

TCGACATGGCGGTCTGACGATCTGACTCGTAGTCGACAACAGGGTAGCCTTCCTCCTCGAATCCGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTCTCT[C/T]
CTGACAGTATCCGGAGACACCGTAGGGTACTAGCCGTGCTTATCCCTGAAGTCGATATCCGGCGGCGTGTCTTGGCGTATGTAGGATTCTATGTTGTGGC

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	91.60%	4.70%	2.81%	0.95%	NA
All Indica	2759	99.20%	0.50%	0.29%	0.00%	NA
All Japonica	1512	76.50%	12.90%	7.67%	2.98%	NA
Aus	269	95.50%	2.20%	2.23%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.60%	0.20%	0.22%	0.00%	NA
Indica Intermediate	786	98.50%	0.90%	0.64%	0.00%	NA
Temperate Japonica	767	91.40%	5.10%	3.26%	0.26%	NA
Tropical Japonica	504	67.70%	20.80%	7.54%	3.97%	NA
Japonica Intermediate	241	47.30%	21.20%	21.99%	9.54%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	5.60%	3.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0322412591	G -> A	LOC_Os03g40310.1	downstream_gene_variant ; 966.0bp to feature; MODIFIER	silent_mutation	Average:58.48; most accessible tissue: Minghui63 root, score: 76.425	N	N	N	N
vg0322412591	G -> A	LOC_Os03g40300-LOC_Os03g40310	intergenic_region ; MODIFIER	silent_mutation	Average:58.48; most accessible tissue: Minghui63 root, score: 76.425	N	N	N	N
vg0322412591	G -> DEL	N	N	silent_mutation	Average:58.48; most accessible tissue: Minghui63 root, score: 76.425	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322412591	2.79E-06	2.79E-06	mr1717	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
vg0322412591	NA	1.27E-07	mr1915	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
vg0322412591	4.52E-06	NA	mr1226_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