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Detailed information for vg1218060310:

Variant ID: vg1218060310 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18060310
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, A: 0.17, T: 0.01, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GAGCTCGGAGCGACACCAAACATCTAAGTTTCTAGACAGTGCATGATCCAACCACTATTGGAGAAACGTTCTTCTGTCCCGGTTTGCAACCCTCTTTACT[A/C]
CTGGATTGCGGTTGAAATAACCGGGACTAAAGGTTAAAATAACCAACCGGGACTAAAGTTTTTTTTTCTTTTCGATTGTTTTTAGTTGCTTGCATGTGTT

Reverse complement sequence

AACACATGCAAGCAACTAAAAACAATCGAAAAGAAAAAAAAACTTTAGTCCCGGTTGGTTATTTTAACCTTTAGTCCCGGTTATTTCAACCGCAATCCAG[T/G]
AGTAAAGAGGGTTGCAAACCGGGACAGAAGAACGTTTCTCCAATAGTGGTTGGATCATGCACTGTCTAGAAACTTAGATGTTTGGTGTCGCTCCGAGCTC

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	57.40%	42.50%	0.13%	0.00%	NA
All Indica	2759	70.20%	29.80%	0.04%	0.00%	NA
All Japonica	1512	37.20%	62.50%	0.33%	0.00%	NA
Aus	269	48.30%	51.70%	0.00%	0.00%	NA
Indica I	595	83.20%	16.80%	0.00%	0.00%	NA
Indica II	465	55.70%	44.10%	0.22%	0.00%	NA
Indica III	913	70.10%	29.90%	0.00%	0.00%	NA
Indica Intermediate	786	69.00%	31.00%	0.00%	0.00%	NA
Temperate Japonica	767	64.10%	35.70%	0.13%	0.00%	NA
Tropical Japonica	504	2.60%	96.80%	0.60%	0.00%	NA
Japonica Intermediate	241	23.70%	75.90%	0.41%	0.00%	NA
VI/Aromatic	96	27.10%	72.90%	0.00%	0.00%	NA
Intermediate	90	64.40%	35.60%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218060310	A -> C	LOC_Os12g30120-LOC_Os12g30130	intergenic_region ; MODIFIER	silent_mutation	Average:35.292; most accessible tissue: Callus, score: 53.312	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218060310	NA	2.33E-07	mr1163	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
vg1218060310	NA	7.85E-07	mr1280	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
vg1218060310	NA	2.14E-06	mr1295	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
vg1218060310	4.73E-06	NA	mr1519	Ind_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
vg1218060310	NA	5.16E-07	mr1617	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
vg1218060310	NA	1.38E-06	mr1902	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