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Detailed information for vg0413297327:

Variant ID: vg0413297327 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13297327
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAATGGGCCACGCTGTGAAAAGTATTGGGCTGAGGTACTTTTCAGGCCTAGGCCCATTTGCACCTCCGATACCCTTAACAAAAAAATCCGAGATCCAAG[C/T]
GACGCTTCGTCTTCCCCGCCGGAACACTTGCCATTTTCCCCACTCCCTGCTACAGTAAAGAGCTGCGCCGGCGAACTAGGGTTCACCAATCCACCCAAAT

Reverse complement sequence

ATTTGGGTGGATTGGTGAACCCTAGTTCGCCGGCGCAGCTCTTTACTGTAGCAGGGAGTGGGGAAAATGGCAAGTGTTCCGGCGGGGAAGACGAAGCGTC[G/A]
CTTGGATCTCGGATTTTTTTGTTAAGGGTATCGGAGGTGCAAATGGGCCTAGGCCTGAAAAGTACCTCAGCCCAATACTTTTCACAGCGTGGCCCATTGT

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	88.50%	1.40%	2.14%	8.00%	NA
All Indica	2759	95.40%	0.00%	0.43%	4.10%	NA
All Japonica	1512	76.00%	4.00%	5.49%	14.48%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	88.70%	0.00%	0.67%	10.59%	NA
Indica II	465	97.80%	0.00%	0.43%	1.72%	NA
Indica III	913	97.50%	0.00%	0.55%	1.97%	NA
Indica Intermediate	786	96.70%	0.10%	0.13%	3.05%	NA
Temperate Japonica	767	93.70%	0.50%	0.39%	5.35%	NA
Tropical Japonica	504	50.00%	10.10%	15.08%	24.80%	NA
Japonica Intermediate	241	73.90%	2.50%	1.66%	21.99%	NA
VI/Aromatic	96	60.40%	0.00%	4.17%	35.42%	NA
Intermediate	90	83.30%	1.10%	2.22%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413297327	C -> DEL	N	N	silent_mutation	Average:7.622; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0413297327	C -> T	LOC_Os04g23290.1	upstream_gene_variant ; 2667.0bp to feature; MODIFIER	silent_mutation	Average:7.622; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0413297327	C -> T	LOC_Os04g23300.1	upstream_gene_variant ; 206.0bp to feature; MODIFIER	silent_mutation	Average:7.622; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0413297327	C -> T	LOC_Os04g23310.1	downstream_gene_variant ; 4028.0bp to feature; MODIFIER	silent_mutation	Average:7.622; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0413297327	C -> T	LOC_Os04g23290-LOC_Os04g23300	intergenic_region ; MODIFIER	silent_mutation	Average:7.622; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413297327	2.19E-06	2.19E-06	mr1254	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