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Detailed information for vg1214134650:

Variant ID: vg1214134650 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14134650
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGGCTGACCGCGATGAGAAACAGATATTGTACGATACAATCGCGGAGGGAAGCAGCCAGTACTGGAATGAAGAAGAGGGAACGAGGATCCAAACCAGTA[C/T]
TTGAACGAGGAAGGGAACGTGGAGAGGGATGCGGAGGGAAACCAGTAGGGGCACGTGGAAAGGGATGTGGAGGGGAACCAGGAGGAGGAGGCTAGTGGTA

Reverse complement sequence

TACCACTAGCCTCCTCCTCCTGGTTCCCCTCCACATCCCTTTCCACGTGCCCCTACTGGTTTCCCTCCGCATCCCTCTCCACGTTCCCTTCCTCGTTCAA[G/A]
TACTGGTTTGGATCCTCGTTCCCTCTTCTTCATTCCAGTACTGGCTGCTTCCCTCCGCGATTGTATCGTACAATATCTGTTTCTCATCGCGGTCAGCCAT

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	19.70%	0.40%	1.71%	78.21%	NA
All Indica	2759	6.00%	0.70%	2.43%	90.83%	NA
All Japonica	1512	47.70%	0.00%	0.53%	51.79%	NA
Aus	269	4.10%	0.00%	0.74%	95.17%	NA
Indica I	595	3.20%	0.50%	1.68%	94.62%	NA
Indica II	465	10.10%	1.50%	2.80%	85.59%	NA
Indica III	913	4.60%	0.10%	3.18%	92.11%	NA
Indica Intermediate	786	7.40%	1.10%	1.91%	89.57%	NA
Temperate Japonica	767	77.20%	0.00%	0.39%	22.43%	NA
Tropical Japonica	504	13.50%	0.00%	0.60%	85.91%	NA
Japonica Intermediate	241	25.30%	0.00%	0.83%	73.86%	NA
VI/Aromatic	96	4.20%	0.00%	1.04%	94.79%	NA
Intermediate	90	30.00%	0.00%	3.33%	66.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214134650	C -> DEL	N	N	silent_mutation	Average:5.671; most accessible tissue: Minghui63 flower, score: 9.27	N	N	N	N
vg1214134650	C -> T	LOC_Os12g24680.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:5.671; most accessible tissue: Minghui63 flower, score: 9.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214134650	1.56E-06	NA	mr1600	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
vg1214134650	9.22E-07	9.22E-07	mr1856	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
vg1214134650	NA	5.47E-08	mr1077_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
vg1214134650	NA	6.82E-07	mr1402_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
vg1214134650	NA	2.12E-06	mr1795_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