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Detailed information for vg0502492380:

Variant ID: vg0502492380 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2492380
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACATCAAAACTTTCCTACACACGGAGTAAACTTCCAACTTTTCCATCATATCGTTCCAATTTTAACCAAATTTCTAATTTTGATATGAACTAAACACAC[C/G]
CTAAGTAGTCTAATTTTTCTTTATGTGTTTGTTTGCGAGGAAGCTTTAAGGAGATGGTTAGTCTCCTGATGATTCTTACATGCTATTCTCATTGCTTTAG

Reverse complement sequence

CTAAAGCAATGAGAATAGCATGTAAGAATCATCAGGAGACTAACCATCTCCTTAAAGCTTCCTCGCAAACAAACACATAAAGAAAAATTAGACTACTTAG[G/C]
GTGTGTTTAGTTCATATCAAAATTAGAAATTTGGTTAAAATTGGAACGATATGATGGAAAAGTTGGAAGTTTACTCCGTGTGTAGGAAAGTTTTGATGTG

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	72.70%	3.30%	14.22%	9.80%	NA
All Indica	2759	65.20%	0.10%	18.67%	16.06%	NA
All Japonica	1512	80.80%	9.80%	9.06%	0.33%	NA
Aus	269	92.90%	0.00%	3.72%	3.35%	NA
Indica I	595	55.00%	0.00%	33.61%	11.43%	NA
Indica II	465	61.30%	0.00%	21.72%	16.99%	NA
Indica III	913	72.00%	0.20%	8.43%	19.39%	NA
Indica Intermediate	786	67.40%	0.00%	17.43%	15.14%	NA
Temperate Japonica	767	65.70%	17.60%	16.04%	0.65%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	89.20%	5.00%	5.81%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	78.90%	4.40%	11.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0502492380	C -> DEL	N	N	silent_mutation	Average:56.745; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0502492380	C -> G	LOC_Os05g05120.1	upstream_gene_variant ; 268.0bp to feature; MODIFIER	silent_mutation	Average:56.745; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0502492380	C -> G	LOC_Os05g05130.1	upstream_gene_variant ; 2602.0bp to feature; MODIFIER	silent_mutation	Average:56.745; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0502492380	C -> G	LOC_Os05g05120-LOC_Os05g05130	intergenic_region ; MODIFIER	silent_mutation	Average:56.745; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502492380	9.70E-08	3.50E-10	mr1588_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