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Detailed information for vg1223766180:

Variant ID: vg1223766180 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23766180
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GGACCAAACATCACAGGCGCGACTTGGGAACTAGGCCGAAACCCTAAAACTCATCGTAGCCGGCTTGCTCCTGGAAGAACTCCTCATCAGTAGGATCCGC[C/T]
TCATCTTCTTCAGCAACTGGGGGGGATTATTTATATAGAGCAAGGGTGAGTACGGGAGTACTCAGCAAGCCATGGGAAATAAGTGTTTAATGCAGGCTTC

Reverse complement sequence

GAAGCCTGCATTAAACACTTATTTCCCATGGCTTGCTGAGTACTCCCGTACTCACCCTTGCTCTATATAAATAATCCCCCCCAGTTGCTGAAGAAGATGA[G/A]
GCGGATCCTACTGATGAGGAGTTCTTCCAGGAGCAAGCCGGCTACGATGAGTTTTAGGGTTTCGGCCTAGTTCCCAAGTCGCGCCTGTGATGTTTGGTCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.50%	0.60%	17.25%	30.62%	NA
All Indica	2759	37.70%	0.40%	19.64%	42.19%	NA
All Japonica	1512	81.00%	0.00%	1.72%	17.33%	NA
Aus	269	10.00%	5.90%	82.53%	1.49%	NA
Indica I	595	15.50%	0.20%	14.96%	69.41%	NA
Indica II	465	28.00%	0.20%	26.88%	44.95%	NA
Indica III	913	53.20%	0.40%	16.32%	30.01%	NA
Indica Intermediate	786	42.40%	0.80%	22.77%	34.10%	NA
Temperate Japonica	767	88.70%	0.00%	0.91%	10.43%	NA
Tropical Japonica	504	77.00%	0.00%	2.78%	20.24%	NA
Japonica Intermediate	241	64.70%	0.00%	2.07%	33.20%	NA
VI/Aromatic	96	89.60%	0.00%	8.33%	2.08%	NA
Intermediate	90	64.40%	0.00%	18.89%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223766180	C -> DEL	N	N	silent_mutation	Average:32.779; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg1223766180	C -> T	LOC_Os12g38690.1	upstream_gene_variant ; 3610.0bp to feature; MODIFIER	silent_mutation	Average:32.779; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg1223766180	C -> T	LOC_Os12g38690-LOC_Os12g38700	intergenic_region ; MODIFIER	silent_mutation	Average:32.779; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223766180	NA	8.58E-06	mr1064	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
vg1223766180	NA	6.88E-09	mr1193	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
vg1223766180	2.24E-06	2.24E-06	mr1750	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
vg1223766180	7.79E-06	3.57E-06	mr1072_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
vg1223766180	5.25E-06	1.31E-06	mr1075_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
vg1223766180	NA	8.53E-06	mr1149_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
vg1223766180	NA	2.76E-11	mr1193_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
vg1223766180	8.22E-06	1.90E-06	mr1344_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
vg1223766180	7.97E-06	NA	mr1381_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
vg1223766180	NA	5.35E-06	mr1511_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
vg1223766180	NA	5.19E-11	mr1722_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
vg1223766180	NA	1.30E-06	mr1727_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
vg1223766180	NA	1.39E-07	mr1804_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
vg1223766180	NA	1.91E-06	mr1861_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