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Detailed information for vg0715468281:

Variant ID: vg0715468281 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15468281
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACGAACCGATGCCTCATAACAAATGCCATTAGGTGAAAACAAAACTACCCCTATGCCTTGACCTTCTTTGCAAGAAGAACCATCAAAATAAATTTTCCA[A/C]
GGTATAACTTCAACTAAGCAAATCTCCCCCTCATAAGCAACATCTATATGATGGTCTACTATAAAATCACATACAATTTGGCCTTTTATAGTTTTCAATG

Reverse complement sequence

CATTGAAAACTATAAAAGGCCAAATTGTATGTGATTTTATAGTAGACCATCATATAGATGTTGCTTATGAGGGGGAGATTTGCTTAGTTGAAGTTATACC[T/G]
TGGAAAATTTATTTTGATGGTTCTTCTTGCAAAGAAGGTCAAGGCATAGGGGTAGTTTTGTTTTCACCTAATGGCATTTGTTATGAGGCATCGGTTCGTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.80%	0.30%	6.67%	41.26%	NA
All Indica	2759	45.00%	0.40%	8.48%	46.10%	NA
All Japonica	1512	55.80%	0.20%	4.23%	39.81%	NA
Aus	269	86.20%	0.00%	2.60%	11.15%	NA
Indica I	595	42.90%	0.00%	3.53%	53.61%	NA
Indica II	465	43.20%	0.00%	8.39%	48.39%	NA
Indica III	913	42.80%	0.80%	12.60%	43.81%	NA
Indica Intermediate	786	50.30%	0.50%	7.51%	41.73%	NA
Temperate Japonica	767	74.60%	0.00%	4.56%	20.86%	NA
Tropical Japonica	504	29.40%	0.60%	4.56%	65.48%	NA
Japonica Intermediate	241	51.00%	0.00%	2.49%	46.47%	NA
VI/Aromatic	96	77.10%	0.00%	6.25%	16.67%	NA
Intermediate	90	62.20%	0.00%	4.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715468281	A -> DEL	N	N	silent_mutation	Average:7.401; most accessible tissue: Callus, score: 30.594	N	N	N	N
vg0715468281	A -> C	LOC_Os07g26780.1	intron_variant ; MODIFIER	silent_mutation	Average:7.401; most accessible tissue: Callus, score: 30.594	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715468281	4.89E-06	4.88E-06	mr1873	Jap_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