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Detailed information for vg0714075702:

Variant ID: vg0714075702 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14075702
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TTAAGTATGGATTTATGTTCTTCGACAGCATTTGGAAGATTGGCTAACTTTTGCTTCTCCAGATCCAACTCAGCATTGCATTCTTCAAGTTGAGCTATTA[G/A]
ATCAATCTTGCGGGCTTCAAGCCGATCTATGTTCGATTGAATCGGACCAGCAGAGAGTTGATCAAGCTTGGCTTTCTCCTCATGCACAAGCTGCCGATTG

Reverse complement sequence

CAATCGGCAGCTTGTGCATGAGGAGAAAGCCAAGCTTGATCAACTCTCTGCTGGTCCGATTCAATCGAACATAGATCGGCTTGAAGCCCGCAAGATTGAT[C/T]
TAATAGCTCAACTTGAAGAATGCAATGCTGAGTTGGATCTGGAGAAGCAAAAGTTAGCCAATCTTCCAAATGCTGTCGAAGAACATAAATCCATACTTAA

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	54.50%	25.70%	8.93%	10.81%	NA
All Indica	2759	37.30%	36.90%	10.91%	14.90%	NA
All Japonica	1512	86.00%	4.70%	3.51%	5.82%	NA
Aus	269	42.80%	38.30%	18.96%	0.00%	NA
Indica I	595	48.40%	27.90%	11.26%	12.44%	NA
Indica II	465	28.00%	33.10%	10.11%	28.82%	NA
Indica III	913	33.00%	47.00%	8.87%	11.17%	NA
Indica Intermediate	786	39.30%	34.40%	13.49%	12.85%	NA
Temperate Japonica	767	88.70%	2.50%	3.78%	5.08%	NA
Tropical Japonica	504	92.70%	2.60%	1.19%	3.57%	NA
Japonica Intermediate	241	63.50%	16.20%	7.47%	12.86%	NA
VI/Aromatic	96	83.30%	10.40%	4.17%	2.08%	NA
Intermediate	90	60.00%	14.40%	14.44%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714075702	G -> DEL	LOC_Os07g24760.1	N	frameshift_variant	Average:19.584; most accessible tissue: Callus, score: 40.125	N	N	N	N
vg0714075702	G -> A	LOC_Os07g24760.1	synonymous_variant ; p.Leu173Leu; LOW	synonymous_codon	Average:19.584; most accessible tissue: Callus, score: 40.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714075702	NA	7.00E-06	mr1177	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
vg0714075702	NA	7.93E-06	mr1374	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
vg0714075702	NA	4.38E-07	mr1516	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
vg0714075702	NA	7.24E-06	mr1563_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
vg0714075702	NA	8.73E-06	mr1982_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