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Detailed information for vg1221198057:

Variant ID: vg1221198057 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21198057
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: 78. )

Flanking Sequence (100 bp) in Reference Genome:

ACCGCGGTTTCTTTGCTTCTATTTCTTGTTGATTACAGGATCAAATCAACTGGCACGCTAGCACACCCGAAGGTGAGCTTTAGACCTGCACTGGAGTTAA[G/A]
CAGATCTCCTAGGTCTCGTGTTTTCTGTCAACACACACACACACACACACACACACATATATATATATATATATATATATATATATATATATATATATAT

Reverse complement sequence

ATATATATATATATATATATATATATATATATATATATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTTGACAGAAAACACGAGACCTAGGAGATCTG[C/T]
TTAACTCCAGTGCAGGTCTAAAGCTCACCTTCGGGTGTGCTAGCGTGCCAGTTGATTTGATCCTGTAATCAACAAGAAATAGAAGCAAAGAAACCGCGGT

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	85.80%	1.20%	2.16%	10.77%	NA
All Indica	2759	83.70%	2.10%	3.26%	10.95%	NA
All Japonica	1512	99.10%	0.00%	0.07%	0.86%	NA
Aus	269	39.00%	0.00%	2.97%	57.99%	NA
Indica I	595	74.80%	3.00%	7.23%	14.96%	NA
Indica II	465	90.10%	1.50%	0.86%	7.53%	NA
Indica III	913	91.00%	0.10%	0.55%	8.32%	NA
Indica Intermediate	786	78.20%	3.90%	4.83%	12.98%	NA
Temperate Japonica	767	99.20%	0.00%	0.13%	0.65%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	63.50%	0.00%	2.08%	34.38%	NA
Intermediate	90	92.20%	1.10%	1.11%	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
vg1221198057	G -> DEL	N	N	silent_mutation	Average:32.567; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg1221198057	G -> A	LOC_Os12g34820.1	downstream_gene_variant ; 2648.0bp to feature; MODIFIER	silent_mutation	Average:32.567; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg1221198057	G -> A	LOC_Os12g34810-LOC_Os12g34820	intergenic_region ; MODIFIER	silent_mutation	Average:32.567; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221198057	5.95E-10	1.30E-16	mr1038	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
vg1221198057	9.81E-10	6.56E-09	mr1141	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
vg1221198057	1.96E-09	5.44E-17	mr1389	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
vg1221198057	2.53E-14	1.46E-19	mr1038_2	Ind_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
vg1221198057	2.29E-14	2.24E-10	mr1141_2	Ind_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
vg1221198057	9.24E-14	8.52E-19	mr1389_2	Ind_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