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Detailed information for vg1213797573:

Variant ID: vg1213797573 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13797573
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGCGTAGCCTTTGCCTGCGCCTCCCTACGGGACGACGACGAGTCAGACAATGCTTGAATGGAATCACGGAAGTCTAAAAATTCATCTACTTACTTCTC[G/A]
CCAATCGTCACAATACGTTGTCGTCGTGGAGGCGGGGGAGACGCGTCCGAGGCCTGACAGACAATCAATGCGAAGTAAGGCAAAATCCTTCTGGCTGCAC

Reverse complement sequence

GTGCAGCCAGAAGGATTTTGCCTTACTTCGCATTGATTGTCTGTCAGGCCTCGGACGCGTCTCCCCCGCCTCCACGACGACAACGTATTGTGACGATTGG[C/T]
GAGAAGTAAGTAGATGAATTTTTAGACTTCCGTGATTCCATTCAAGCATTGTCTGACTCGTCGTCGTCCCGTAGGGAGGCGCAGGCAAAGGCTACGCGAG

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	73.90%	16.00%	1.67%	8.44%	NA
All Indica	2759	71.00%	21.70%	1.78%	5.51%	NA
All Japonica	1512	91.00%	0.20%	0.33%	8.47%	NA
Aus	269	26.00%	24.90%	6.32%	42.75%	NA
Indica I	595	87.60%	2.70%	2.02%	7.73%	NA
Indica II	465	84.10%	6.90%	2.37%	6.67%	NA
Indica III	913	49.80%	46.40%	1.42%	2.30%	NA
Indica Intermediate	786	75.30%	16.20%	1.65%	6.87%	NA
Temperate Japonica	767	88.00%	0.00%	0.65%	11.34%	NA
Tropical Japonica	504	97.00%	0.20%	0.00%	2.78%	NA
Japonica Intermediate	241	88.00%	0.80%	0.00%	11.20%	NA
VI/Aromatic	96	12.50%	77.10%	8.33%	2.08%	NA
Intermediate	90	85.60%	12.20%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213797573	G -> DEL	LOC_Os12g24210.1	N	frameshift_variant	Average:19.129; most accessible tissue: Callus, score: 47.902	N	N	N	N
vg1213797573	G -> A	LOC_Os12g24210.1	synonymous_variant ; p.Gly321Gly; LOW	synonymous_codon	Average:19.129; most accessible tissue: Callus, score: 47.902	N	N	N	N
vg1213797573	G -> A	LOC_Os12g24210.1	synonymous_variant ; p.Gly321Gly; LOW	nonsynonymous_codon ; G321S	Average:19.129; most accessible tissue: Callus, score: 47.902	possibly damaging	1.716	TOLERATED	0.14

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213797573	7.32E-08	NA	mr1129	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
vg1213797573	NA	8.87E-07	mr1169	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
vg1213797573	4.66E-06	NA	mr1251	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
vg1213797573	7.69E-08	5.28E-17	mr1253	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
vg1213797573	4.84E-07	NA	mr1255	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
vg1213797573	4.56E-07	NA	mr1257	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
vg1213797573	NA	7.65E-07	mr1377	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
vg1213797573	6.57E-06	NA	mr1423	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
vg1213797573	8.95E-06	NA	mr1435	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
vg1213797573	3.23E-06	NA	mr1129_2	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
vg1213797573	NA	3.39E-07	mr1138_2	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
vg1213797573	1.86E-07	NA	mr1255_2	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
vg1213797573	7.00E-06	NA	mr1257_2	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
vg1213797573	NA	7.07E-06	mr1908_2	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