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Detailed information for vg1218075103:

Variant ID: vg1218075103 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18075103
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GATTAGACGATGAGGATGGAACTAGATAAATCATGGAATTGCGCAAGCATCATGGTGTTGTGTGCATCTACAATTGGAGCCCATAACAGAATTATCATTA[A/C]
AATGTTAAAAGTGCCATGAGAATGAGAGGTATTCATGAAACAAGTCAGAAGCCCAATATGCTTTTCTATCCGATTACGCTTGCAAGTTCAGGATTACCAA

Reverse complement sequence

TTGGTAATCCTGAACTTGCAAGCGTAATCGGATAGAAAAGCATATTGGGCTTCTGACTTGTTTCATGAATACCTCTCATTCTCATGGCACTTTTAACATT[T/G]
TAATGATAATTCTGTTATGGGCTCCAATTGTAGATGCACACAACACCATGATGCTTGCGCAATTCCATGATTTATCTAGTTCCATCCTCATCGTCTAATC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.50%	7.60%	0.40%	3.43%	NA
All Indica	2759	86.10%	12.60%	0.11%	1.16%	NA
All Japonica	1512	99.20%	0.60%	0.07%	0.13%	NA
Aus	269	56.10%	0.40%	4.46%	39.03%	NA
Indica I	595	92.90%	7.10%	0.00%	0.00%	NA
Indica II	465	92.50%	7.10%	0.00%	0.43%	NA
Indica III	913	81.60%	16.10%	0.11%	2.19%	NA
Indica Intermediate	786	82.30%	16.20%	0.25%	1.27%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	2.90%	0.41%	0.83%	NA
VI/Aromatic	96	80.20%	0.00%	2.08%	17.71%	NA
Intermediate	90	90.00%	2.20%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218075103	A -> C	LOC_Os12g30130-LOC_Os12g30140	intergenic_region ; MODIFIER	silent_mutation	Average:41.449; most accessible tissue: Zhenshan97 flower, score: 69.437	N	N	N	N
vg1218075103	A -> DEL	N	N	silent_mutation	Average:41.449; most accessible tissue: Zhenshan97 flower, score: 69.437	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218075103	9.37E-06	9.39E-06	mr1273	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
vg1218075103	8.10E-06	8.10E-06	mr1273	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
vg1218075103	1.64E-06	1.64E-06	mr1321	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
vg1218075103	3.18E-06	3.17E-06	mr1340	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