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Detailed information for vg1217448754:

Variant ID: vg1217448754 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17448754
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTCGCCGGTTTCGGTTGATCATTTGGGTGATCCCGTGTCACGTAGAATTGACTCGTTGAGTCGGTATCTCGTGAGGTTCGCTTGCAAGATTAATCTTA[G/A]
CCATCCAAAATCAATATAAATCATTTCCTCTCTTTTCAGTGGCATATTATTTCTTTTTAATATATGTCATCTACCAAATATAGTCTAATCTATTTCCGGA

Reverse complement sequence

TCCGGAAATAGATTAGACTATATTTGGTAGATGACATATATTAAAAAGAAATAATATGCCACTGAAAAGAGAGGAAATGATTTATATTGATTTTGGATGG[C/T]
TAAGATTAATCTTGCAAGCGAACCTCACGAGATACCGACTCAACGAGTCAATTCTACGTGACACGGGATCACCCAAATGATCAACCGAAACCGGCGAACG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.80%	1.80%	0.72%	5.71%	NA
All Indica	2759	94.20%	0.10%	0.29%	5.40%	NA
All Japonica	1512	87.40%	5.40%	1.59%	5.62%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	95.80%	0.00%	0.34%	3.87%	NA
Indica II	465	98.90%	0.00%	0.00%	1.08%	NA
Indica III	913	90.40%	0.00%	0.44%	9.20%	NA
Indica Intermediate	786	94.70%	0.40%	0.25%	4.71%	NA
Temperate Japonica	767	85.80%	9.90%	1.30%	3.00%	NA
Tropical Japonica	504	90.10%	0.00%	0.99%	8.93%	NA
Japonica Intermediate	241	87.10%	2.10%	3.73%	7.05%	NA
VI/Aromatic	96	68.80%	0.00%	1.04%	30.21%	NA
Intermediate	90	91.10%	1.10%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217448754	G -> DEL	N	N	silent_mutation	Average:50.814; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1217448754	G -> A	LOC_Os12g29380.1	downstream_gene_variant ; 4605.0bp to feature; MODIFIER	silent_mutation	Average:50.814; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1217448754	G -> A	LOC_Os12g29370-LOC_Os12g29380	intergenic_region ; MODIFIER	silent_mutation	Average:50.814; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217448754	2.89E-06	2.21E-07	mr1616	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
vg1217448754	NA	5.83E-06	mr1697	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
vg1217448754	NA	3.34E-06	mr1851	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
vg1217448754	1.20E-06	1.20E-06	mr1004_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
vg1217448754	NA	8.06E-07	mr1296_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
vg1217448754	NA	3.50E-06	mr1358_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