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Detailed information for vg0717838198:

Variant ID: vg0717838198 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 17838198
Reference Allele: C	Alternative Allele: G,A
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCCTTTACAGGTTATTTTTTTAACTATCCACTTCCTTCGTACCTGGGCTATCCTTCAGAAGCCTGGTTCACGGGATTTGGTTGCAGCGGCGTGTCAGC[C/G,A]
CTTGGAGCAGGTGGTCAGGGAATGTTTTACCCAGGGACATGGGTGGCGGTCTAGCTTGAAGATTGGTGCTCCCTGATTTTTACTGCTTTCCTTCTATTGT

Reverse complement sequence

ACAATAGAAGGAAAGCAGTAAAAATCAGGGAGCACCAATCTTCAAGCTAGACCGCCACCCATGTCCCTGGGTAAAACATTCCCTGACCACCTGCTCCAAG[G/C,T]
GCTGACACGCCGCTGCAACCAAATCCCGTGAACCAGGCTTCTGAAGGATAGCCCAGGTACGAAGGAAGTGGATAGTTAAAAAAATAACCTGTAAAGGAGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.10%	34.90%	0.99%	0.00%	NA
All Indica	2759	48.50%	49.90%	1.63%	0.00%	NA
All Japonica	1512	89.20%	10.80%	0.07%	0.00%	NA
Aus	269	71.40%	28.30%	0.37%	0.00%	NA
Indica I	595	82.70%	14.60%	2.69%	0.00%	NA
Indica II	465	22.40%	76.30%	1.29%	0.00%	NA
Indica III	913	37.10%	62.40%	0.44%	0.00%	NA
Indica Intermediate	786	51.10%	46.40%	2.42%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	75.40%	24.40%	0.20%	0.00%	NA
Japonica Intermediate	241	86.30%	13.70%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	67.80%	32.20%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0717838198	C -> G	LOC_Os07g30190.1	missense_variant ; p.Pro1611Arg; MODERATE	nonsynonymous_codon ; P1611R	Average:55.712; most accessible tissue: Callus, score: 85.209	unknown	unknown	TOLERATED	0.31
vg0717838198	C -> A	LOC_Os07g30190.1	missense_variant ; p.Pro1611His; MODERATE	N	Average:55.712; most accessible tissue: Callus, score: 85.209	N	N	N	N
vg0717838198	C -> A	LOC_Os07g30200.1	upstream_gene_variant ; 327.0bp to feature; MODIFIER	N	Average:55.712; most accessible tissue: Callus, score: 85.209	N	N	N	N
vg0717838198	C -> A	LOC_Os07g30200.2	upstream_gene_variant ; 327.0bp to feature; MODIFIER	N	Average:55.712; most accessible tissue: Callus, score: 85.209	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0717838198	1.10E-06	2.97E-07	mr1090_2	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
vg0717838198	NA	3.54E-06	mr1211_2	Jap_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