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Detailed information for vg0720025470:

Variant ID: vg0720025470 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 20025470
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

AGTAGTCCATGAACACTTTGTTCATAAGATTCATAAAGTATGCCGGAGCGTTGGTTAAACCAAACGACATTACGGTGAACTCATATAATCCATAGCATGT[T/G]
GAGAACGCGGTTTTGGGTATGTCCCCGGTTCTAATTTTCAATTGGTGGTATCCTGACCGAAGGTCAATCTTAGAGAACACCTTAGCTCCGTTGAGTTGAT

Reverse complement sequence

ATCAACTCAACGGAGCTAAGGTGTTCTCTAAGATTGACCTTCGGTCAGGATACCACCAATTGAAAATTAGAACCGGGGACATACCCAAAACCGCGTTCTC[A/C]
ACATGCTATGGATTATATGAGTTCACCGTAATGTCGTTTGGTTTAACCAACGCTCCGGCATACTTTATGAATCTTATGAACAAAGTGTTCATGGACTACT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.20%	11.90%	10.81%	6.07%	NA
All Indica	2759	73.80%	14.70%	11.02%	0.47%	NA
All Japonica	1512	64.70%	9.90%	7.61%	17.79%	NA
Aus	269	85.90%	0.40%	13.75%	0.00%	NA
Indica I	595	89.70%	2.20%	8.07%	0.00%	NA
Indica II	465	57.60%	17.00%	23.44%	1.94%	NA
Indica III	913	68.30%	25.00%	6.68%	0.00%	NA
Indica Intermediate	786	77.60%	10.90%	10.94%	0.51%	NA
Temperate Japonica	767	95.30%	0.30%	0.39%	4.04%	NA
Tropical Japonica	504	17.10%	28.00%	19.05%	35.91%	NA
Japonica Intermediate	241	66.80%	2.90%	6.64%	23.65%	NA
VI/Aromatic	96	59.40%	1.00%	37.50%	2.08%	NA
Intermediate	90	70.00%	5.60%	21.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0720025470	T -> DEL	LOC_Os07g33500.1	N	frameshift_variant	Average:26.948; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N
vg0720025470	T -> G	LOC_Os07g33500.1	synonymous_variant ; p.Ser653Ser; LOW	synonymous_codon	Average:26.948; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720025470	3.09E-06	NA	mr1439	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
vg0720025470	NA	8.56E-06	mr1607	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
vg0720025470	NA	2.53E-07	mr1993	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