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Detailed information for vg0711204473:

Variant ID: vg0711204473 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11204473
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCACTTTCCAACCCTTCCTTTCAAAATTGGAGCCGATAACATGTATTTGACAACATTGGCCTTGAATATGACAGTACACTCGTTGGATAGTAGATAATG[C/T]
CTCAACCTTATACTTGAAAAATATAAGCACAAGCATAACTTCTCCACAGGGGAATATCTAGTTTCTGCATCCAAGAGCCAACGACTGAGATAGAATACAA

Reverse complement sequence

TTGTATTCTATCTCAGTCGTTGGCTCTTGGATGCAGAAACTAGATATTCCCCTGTGGAGAAGTTATGCTTGTGCTTATATTTTTCAAGTATAAGGTTGAG[G/A]
CATTATCTACTATCCAACGAGTGTACTGTCATATTCAAGGCCAATGTTGTCAAATACATGTTATCGGCTCCAATTTTGAAAGGAAGGGTTGGAAAGTGAA

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	53.90%	0.10%	24.86%	21.12%	NA
All Indica	2759	39.20%	0.20%	35.74%	24.86%	NA
All Japonica	1512	81.10%	0.00%	3.44%	15.48%	NA
Aus	269	59.10%	0.00%	33.46%	7.43%	NA
Indica I	595	28.20%	0.00%	38.32%	33.45%	NA
Indica II	465	38.90%	0.20%	30.97%	29.89%	NA
Indica III	913	43.70%	0.20%	35.49%	20.59%	NA
Indica Intermediate	786	42.50%	0.30%	36.90%	20.36%	NA
Temperate Japonica	767	77.10%	0.00%	5.74%	17.21%	NA
Tropical Japonica	504	87.10%	0.00%	0.60%	12.30%	NA
Japonica Intermediate	241	81.30%	0.00%	2.07%	16.60%	NA
VI/Aromatic	96	33.30%	0.00%	27.08%	39.58%	NA
Intermediate	90	54.40%	0.00%	23.33%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711204473	C -> DEL	N	N	silent_mutation	Average:13.41; most accessible tissue: Callus, score: 27.212	N	N	N	N
vg0711204473	C -> T	LOC_Os07g18900.1	downstream_gene_variant ; 1366.0bp to feature; MODIFIER	silent_mutation	Average:13.41; most accessible tissue: Callus, score: 27.212	N	N	N	N
vg0711204473	C -> T	LOC_Os07g18920.1	downstream_gene_variant ; 969.0bp to feature; MODIFIER	silent_mutation	Average:13.41; most accessible tissue: Callus, score: 27.212	N	N	N	N
vg0711204473	C -> T	LOC_Os07g18910.1	intron_variant ; MODIFIER	silent_mutation	Average:13.41; most accessible tissue: Callus, score: 27.212	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711204473	3.65E-06	NA	mr1398	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
vg0711204473	NA	7.41E-06	mr1756_2	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