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Detailed information for vg1216258965:

Variant ID: vg1216258965 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16258965
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

GGTCTTTCTCTCTCTAAATATACAGTATATATACAACGACTTAGTGAATGCGCACAGTCTTGCCTGGGTCTGATCCATCAATATATGGTGACAATGGTAT[C/G]
GATGCACTAAAAGAGCAATCTGCTGCTCAAGTTCGGTTCGTAGCTAACGAAAAATGCTTGGTGTGATTGAGATCCTAGTTGGGAATGGAAGGAATCAAGA

Reverse complement sequence

TCTTGATTCCTTCCATTCCCAACTAGGATCTCAATCACACCAAGCATTTTTCGTTAGCTACGAACCGAACTTGAGCAGCAGATTGCTCTTTTAGTGCATC[G/C]
ATACCATTGTCACCATATATTGATGGATCAGACCCAGGCAAGACTGTGCGCATTCACTAAGTCGTTGTATATATACTGTATATTTAGAGAGAGAAAGACC

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	56.80%	1.30%	14.49%	27.42%	NA
All Indica	2759	47.30%	1.70%	16.20%	34.76%	NA
All Japonica	1512	72.90%	0.90%	14.09%	12.10%	NA
Aus	269	46.10%	0.00%	2.97%	50.93%	NA
Indica I	595	76.00%	1.50%	9.92%	12.61%	NA
Indica II	465	38.70%	2.80%	13.55%	44.95%	NA
Indica III	913	30.40%	0.90%	22.89%	45.78%	NA
Indica Intermediate	786	50.30%	2.30%	14.76%	32.70%	NA
Temperate Japonica	767	98.30%	0.00%	0.78%	0.91%	NA
Tropical Japonica	504	29.00%	2.20%	37.90%	30.95%	NA
Japonica Intermediate	241	84.20%	0.80%	6.64%	8.30%	NA
VI/Aromatic	96	92.70%	0.00%	3.12%	4.17%	NA
Intermediate	90	68.90%	1.10%	15.56%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216258965	C -> DEL	N	N	silent_mutation	Average:52.565; most accessible tissue: Minghui63 flag leaf, score: 81.052	N	N	N	N
vg1216258965	C -> G	LOC_Os12g27630.1	downstream_gene_variant ; 3750.0bp to feature; MODIFIER	silent_mutation	Average:52.565; most accessible tissue: Minghui63 flag leaf, score: 81.052	N	N	N	N
vg1216258965	C -> G	LOC_Os12g27610-LOC_Os12g27630	intergenic_region ; MODIFIER	silent_mutation	Average:52.565; most accessible tissue: Minghui63 flag leaf, score: 81.052	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216258965	NA	4.61E-07	mr1304	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
vg1216258965	3.79E-06	4.27E-09	mr1364	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
vg1216258965	NA	9.58E-06	mr1364	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
vg1216258965	NA	6.41E-06	mr1382	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
vg1216258965	NA	3.01E-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
vg1216258965	4.05E-06	2.59E-09	mr1443	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
vg1216258965	NA	8.10E-08	mr1551	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
vg1216258965	NA	2.36E-07	mr1659	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
vg1216258965	NA	1.44E-08	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
vg1216258965	NA	8.16E-06	mr1700	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
vg1216258965	NA	5.73E-06	mr1892	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
vg1216258965	NA	6.69E-07	mr1257_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
vg1216258965	NA	9.87E-08	mr1526_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
vg1216258965	NA	7.06E-06	mr1815_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