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Detailed information for vg0715141062:

Variant ID: vg0715141062 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15141062
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTATAAACAGAAGTTTAAAGAAGTAAACAGTTGTAATAATTAATCAATATTAATCATCCGCTGTCCAACGCTATCCCACATTGCAACAGGCCCAACCATC[C/A]
ACCTATACTATCCAATTTCATTAGACTAAACTAGGGTGAGTCTAATCACGGTGAATCTGGTTGACCGCCCATAACCGCGGGCACGGCTATTTGAATAGTT

Reverse complement sequence

AACTATTCAAATAGCCGTGCCCGCGGTTATGGGCGGTCAACCAGATTCACCGTGATTAGACTCACCCTAGTTTAGTCTAATGAAATTGGATAGTATAGGT[G/T]
GATGGTTGGGCCTGTTGCAATGTGGGATAGCGTTGGACAGCGGATGATTAATATTGATTAATTATTACAACTGTTTACTTCTTTAAACTTCTGTTTATAA

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	92.80%	0.30%	1.21%	5.71%	NA
All Indica	2759	91.30%	0.40%	1.63%	6.67%	NA
All Japonica	1512	97.80%	0.00%	0.20%	1.98%	NA
Aus	269	85.90%	0.40%	2.97%	10.78%	NA
Indica I	595	92.30%	0.20%	0.84%	6.72%	NA
Indica II	465	92.70%	0.40%	1.08%	5.81%	NA
Indica III	913	90.70%	0.30%	2.08%	6.90%	NA
Indica Intermediate	786	90.30%	0.80%	2.04%	6.87%	NA
Temperate Japonica	767	95.70%	0.00%	0.39%	3.91%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	77.10%	0.00%	0.00%	22.92%	NA
Intermediate	90	92.20%	1.10%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715141062	C -> DEL	N	N	silent_mutation	Average:12.151; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0715141062	C -> A	LOC_Os07g26350.1	upstream_gene_variant ; 1779.0bp to feature; MODIFIER	silent_mutation	Average:12.151; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0715141062	C -> A	LOC_Os07g26340.1	downstream_gene_variant ; 2562.0bp to feature; MODIFIER	silent_mutation	Average:12.151; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0715141062	C -> A	LOC_Os07g26340-LOC_Os07g26350	intergenic_region ; MODIFIER	silent_mutation	Average:12.151; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715141062	NA	9.03E-09	mr1332	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
vg0715141062	1.85E-06	2.83E-07	mr1332	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