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Detailed information for vg1014028348:

Variant ID: vg1014028348 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14028348
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGGACAGGGGCGGTGGCGGTGGACGAGATGGGTCCAGTAGCAGCGGTGTTTGGGACTGCGGGTCTACTTCATGTGTTTTTCCTATTCCTCCGTTTTTT[C/A]
TACCCTGCGATTCAAAGGGGCCCTAAACTTCCTACAAACGCTCTCAAGCCACCACGTGGTATCCCTAAAAATGCTCCTAGACCGTCATGTGGCATTCTAA

Reverse complement sequence

TTAGAATGCCACATGACGGTCTAGGAGCATTTTTAGGGATACCACGTGGTGGCTTGAGAGCGTTTGTAGGAAGTTTAGGGCCCCTTTGAATCGCAGGGTA[G/T]
AAAAAACGGAGGAATAGGAAAAACACATGAAGTAGACCCGCAGTCCCAAACACCGCTGCTACTGGACCCATCTCGTCCACCGCCACCGCCCCTGTCCTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.00%	8.10%	30.72%	35.23%	NA
All Indica	2759	1.20%	0.20%	44.07%	54.51%	NA
All Japonica	1512	70.80%	23.50%	5.22%	0.40%	NA
Aus	269	0.00%	0.40%	47.96%	51.67%	NA
Indica I	595	0.80%	0.00%	22.86%	76.30%	NA
Indica II	465	2.40%	0.20%	41.08%	56.34%	NA
Indica III	913	0.10%	0.10%	61.56%	38.23%	NA
Indica Intermediate	786	2.20%	0.40%	41.60%	55.85%	NA
Temperate Japonica	767	79.40%	13.60%	6.91%	0.13%	NA
Tropical Japonica	504	74.40%	23.40%	1.59%	0.60%	NA
Japonica Intermediate	241	36.10%	55.60%	7.47%	0.83%	NA
VI/Aromatic	96	86.50%	11.50%	1.04%	1.04%	NA
Intermediate	90	43.30%	10.00%	30.00%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1014028348	C -> A	LOC_Os10g26780-LOC_Os10g26800	intergenic_region ; MODIFIER	silent_mutation	Average:56.31; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N
vg1014028348	C -> DEL	N	N	silent_mutation	Average:56.31; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014028348	NA	2.72E-07	mr1205_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
vg1014028348	1.99E-06	NA	mr1502_2	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
vg1014028348	NA	2.32E-06	mr1662_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
vg1014028348	2.83E-07	3.04E-10	mr1680_2	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
vg1014028348	1.03E-06	NA	mr1871_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