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Detailed information for vg0714931175:

Variant ID: vg0714931175 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14931175
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: 81. )

Flanking Sequence (100 bp) in Reference Genome:

CAACGGGCAGCCCCCCTTTCGTGCAGCGGTGAATCCGGAAGCCGATCAACCGGACACCCCGGCCGACCCAACTCCATCACGCCCACCCTCACCTGGGTAC[G/A]
TCGGCTAGAGGAAAGCTACACTACAAGCCCAGCCGTTGCCCACGCTGACTTGTGGTAAGTACGATAAGTTCTTCCAGGGCATCCCGCGAACCGGTCCTTT

Reverse complement sequence

AAAGGACCGGTTCGCGGGATGCCCTGGAAGAACTTATCGTACTTACCACAAGTCAGCGTGGGCAACGGCTGGGCTTGTAGTGTAGCTTTCCTCTAGCCGA[C/T]
GTACCCAGGTGAGGGTGGGCGTGATGGAGTTGGGTCGGCCGGGGTGTCCGGTTGATCGGCTTCCGGATTCACCGCTGCACGAAAGGGGGGCTGCCCGTTG

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	73.00%	8.30%	17.67%	0.95%	NA
All Indica	2759	58.00%	12.30%	28.13%	1.56%	NA
All Japonica	1512	97.30%	1.40%	1.26%	0.07%	NA
Aus	269	90.30%	0.00%	9.67%	0.00%	NA
Indica I	595	58.30%	7.40%	32.61%	1.68%	NA
Indica II	465	59.60%	14.60%	23.87%	1.94%	NA
Indica III	913	60.70%	14.30%	23.77%	1.20%	NA
Indica Intermediate	786	53.70%	12.30%	32.32%	1.65%	NA
Temperate Japonica	767	98.40%	0.00%	1.56%	0.00%	NA
Tropical Japonica	504	96.00%	3.20%	0.60%	0.20%	NA
Japonica Intermediate	241	96.30%	2.10%	1.66%	0.00%	NA
VI/Aromatic	96	70.80%	25.00%	4.17%	0.00%	NA
Intermediate	90	77.80%	10.00%	11.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714931175	G -> DEL	N	N	silent_mutation	Average:10.679; most accessible tissue: Callus, score: 22.952	N	N	N	N
vg0714931175	G -> A	LOC_Os07g26030.1	downstream_gene_variant ; 1833.0bp to feature; MODIFIER	silent_mutation	Average:10.679; most accessible tissue: Callus, score: 22.952	N	N	N	N
vg0714931175	G -> A	LOC_Os07g26020.1	intron_variant ; MODIFIER	silent_mutation	Average:10.679; most accessible tissue: Callus, score: 22.952	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714931175	8.04E-07	5.42E-07	mr1114	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
vg0714931175	9.36E-06	NA	mr1116	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