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Detailed information for vg0714224732:

Variant ID: vg0714224732 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14224732
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATTCGACTTCTATTTATAAATGCCAGTATTATGCAAATGAACCTGTATAGCTATCCCTTGTTGAATCCCTGCATCATACCCCCATTCCGGTATGACTTG[C/T]
TGAGTACAGTGGATAGTACTCAGTCTTGCTTTATTTTCCCCCAACCCCAGAGTGTGAGTATGTGTCTGATGGCGGGTTCTCCGAGGAGTAGGCTTCGTCC

Reverse complement sequence

GGACGAAGCCTACTCCTCGGAGAACCCGCCATCAGACACATACTCACACTCTGGGGTTGGGGGAAAATAAAGCAAGACTGAGTACTATCCACTGTACTCA[G/A]
CAAGTCATACCGGAATGGGGGTATGATGCAGGGATTCAACAAGGGATAGCTATACAGGTTCATTTGCATAATACTGGCATTTATAAATAGAAGTCGAATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.40%	0.00%	1.29%	23.25%	NA
All Indica	2759	82.60%	0.10%	1.38%	15.95%	NA
All Japonica	1512	58.70%	0.00%	1.06%	40.21%	NA
Aus	269	90.70%	0.00%	0.74%	8.55%	NA
Indica I	595	79.70%	0.00%	1.51%	18.82%	NA
Indica II	465	76.30%	0.00%	1.51%	22.15%	NA
Indica III	913	86.90%	0.10%	1.20%	11.83%	NA
Indica Intermediate	786	83.60%	0.10%	1.40%	14.89%	NA
Temperate Japonica	767	74.60%	0.00%	0.65%	24.77%	NA
Tropical Japonica	504	32.10%	0.00%	1.79%	66.07%	NA
Japonica Intermediate	241	63.90%	0.00%	0.83%	35.27%	NA
VI/Aromatic	96	88.50%	0.00%	1.04%	10.42%	NA
Intermediate	90	75.60%	0.00%	4.44%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714224732	C -> DEL	N	N	silent_mutation	Average:9.112; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0714224732	C -> T	LOC_Os07g24980.1	upstream_gene_variant ; 820.0bp to feature; MODIFIER	silent_mutation	Average:9.112; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0714224732	C -> T	LOC_Os07g24990.1	upstream_gene_variant ; 2051.0bp to feature; MODIFIER	silent_mutation	Average:9.112; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0714224732	C -> T	LOC_Os07g24970-LOC_Os07g24980	intergenic_region ; MODIFIER	silent_mutation	Average:9.112; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714224732	1.22E-06	NA	mr1719	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