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Detailed information for vg0724674424:

Variant ID: vg0724674424 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24674424
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATATAACTATAAATAAAAATTAAATATTTTAATACACAAACTCAACAAATAGCTTAGAACGGAATTTAATTAAGCGATACATTAGGAGAAACTTTTTT[A/T]
AAAAAAAGTATTTTTAGAGGTGTCAAACGAATAATCTGCGACAATTATCCAGTGAAGCAGAACAGGTAAAGTAAACATGATCTATGTTTTTTTCCTCTGT

Reverse complement sequence

ACAGAGGAAAAAAACATAGATCATGTTTACTTTACCTGTTCTGCTTCACTGGATAATTGTCGCAGATTATTCGTTTGACACCTCTAAAAATACTTTTTTT[T/A]
AAAAAAGTTTCTCCTAATGTATCGCTTAATTAAATTCCGTTCTAAGCTATTTGTTGAGTTTGTGTATTAAAATATTTAATTTTTATTTATAGTTATATGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.50%	7.10%	1.97%	19.36%	NA
All Indica	2759	94.20%	2.70%	0.72%	2.39%	NA
All Japonica	1512	34.60%	17.00%	1.12%	47.29%	NA
Aus	269	53.90%	0.00%	14.13%	31.97%	NA
Indica I	595	98.20%	1.20%	0.50%	0.17%	NA
Indica II	465	91.60%	0.60%	0.00%	7.74%	NA
Indica III	913	97.40%	2.20%	0.22%	0.22%	NA
Indica Intermediate	786	88.90%	5.70%	1.91%	3.44%	NA
Temperate Japonica	767	58.80%	32.20%	1.17%	7.82%	NA
Tropical Japonica	504	6.30%	0.20%	0.60%	92.86%	NA
Japonica Intermediate	241	16.60%	3.70%	2.07%	77.59%	NA
VI/Aromatic	96	63.50%	0.00%	13.54%	22.92%	NA
Intermediate	90	60.00%	5.60%	5.56%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0724674424	A -> DEL	N	N	silent_mutation	Average:58.703; most accessible tissue: Minghui63 flower, score: 73.972	N	N	N	N
vg0724674424	A -> T	LOC_Os07g41200-LOC_Os07g41210	intergenic_region ; MODIFIER	silent_mutation	Average:58.703; most accessible tissue: Minghui63 flower, score: 73.972	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724674424	4.94E-06	2.53E-08	mr1354_2	Ind_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
vg0724674424	NA	9.18E-06	mr1528_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
vg0724674424	NA	5.13E-06	mr1528_2	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