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Detailed information for vg1216321299:

Variant ID: vg1216321299 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16321299
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTCGATTTCCAAAAAAAACTTGTGAAAAAGATTGAGTGGATTTGATGAGTAGAGATGGGGGGGAGAGAGGGGAGAAGGGCTTCTCTGCGTGCTCGGGC[T/C]
CCTAAGTTGGCGAAAATGAGTGGGGGAGGAGAAAGGAGGTGGGGCCCGCACGGGTTAAGGGCGCGGCCCACCCAGGGGGAGTGCGGCAGCCTTGCTAGCA

Reverse complement sequence

TGCTAGCAAGGCTGCCGCACTCCCCCTGGGTGGGCCGCGCCCTTAACCCGTGCGGGCCCCACCTCCTTTCTCCTCCCCCACTCATTTTCGCCAACTTAGG[A/G]
GCCCGAGCACGCAGAGAAGCCCTTCTCCCCTCTCTCCCCCCCATCTCTACTCATCAAATCCACTCAATCTTTTTCACAAGTTTTTTTTGGAAATCGAAGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.10%	1.80%	2.77%	17.39%	NA
All Indica	2759	82.90%	0.40%	0.87%	15.84%	NA
All Japonica	1512	69.40%	4.70%	6.02%	19.91%	NA
Aus	269	77.70%	0.00%	1.86%	20.45%	NA
Indica I	595	91.60%	0.00%	0.17%	8.24%	NA
Indica II	465	58.50%	2.40%	3.66%	35.48%	NA
Indica III	913	90.80%	0.00%	0.11%	9.09%	NA
Indica Intermediate	786	81.40%	0.10%	0.64%	17.81%	NA
Temperate Japonica	767	96.10%	0.00%	0.39%	3.52%	NA
Tropical Japonica	504	22.40%	13.50%	16.07%	48.02%	NA
Japonica Intermediate	241	82.60%	1.20%	2.90%	13.28%	NA
VI/Aromatic	96	77.10%	0.00%	2.08%	20.83%	NA
Intermediate	90	78.90%	1.10%	10.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216321299	T -> C	LOC_Os12g27680-LOC_Os12g27690	intergenic_region ; MODIFIER	silent_mutation	Average:45.868; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N
vg1216321299	T -> DEL	N	N	silent_mutation	Average:45.868; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216321299	NA	2.41E-06	mr1036	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
vg1216321299	5.70E-06	5.70E-06	mr1131	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
vg1216321299	2.05E-06	NA	mr1156	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
vg1216321299	1.36E-06	NA	mr1236	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
vg1216321299	NA	8.64E-08	mr1382	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
vg1216321299	7.08E-06	NA	mr1386	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
vg1216321299	NA	1.66E-06	mr1414	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
vg1216321299	4.02E-06	NA	mr1491	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
vg1216321299	1.23E-07	3.20E-11	mr1696	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
vg1216321299	NA	3.39E-09	mr1696	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
vg1216321299	NA	2.76E-06	mr1697	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
vg1216321299	3.18E-06	NA	mr1022_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
vg1216321299	2.16E-06	NA	mr1023_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
vg1216321299	1.39E-06	NA	mr1055_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
vg1216321299	5.92E-07	NA	mr1079_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
vg1216321299	6.34E-06	NA	mr1132_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
vg1216321299	2.17E-07	NA	mr1390_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
vg1216321299	4.39E-06	NA	mr1489_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