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Detailed information for vg1216422805:

Variant ID: vg1216422805 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16422805
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACGCGCAGCTGTGGAGGCGAACAAACCAGTCGGCATCAGACAAGGCGGCCAACAATGAAGACGATGACGTCCATCAGTAGTGGTAGCGGTATAAACCAG[C/A]
CGTAGAGGCGAGGGCACTAGTCAGCTGCAGACGAGATGACCGGCGGTGAAGACGATAAGGCCAATCAACACTAGCAGAATCATGCAGCCATGGAAGTGAT

Reverse complement sequence

ATCACTTCCATGGCTGCATGATTCTGCTAGTGTTGATTGGCCTTATCGTCTTCACCGCCGGTCATCTCGTCTGCAGCTGACTAGTGCCCTCGCCTCTACG[G/T]
CTGGTTTATACCGCTACCACTACTGATGGACGTCATCGTCTTCATTGTTGGCCGCCTTGTCTGATGCCGACTGGTTTGTTCGCCTCCACAGCTGCGCGTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.20%	0.30%	6.37%	56.09%	NA
All Indica	2759	16.20%	0.50%	6.96%	76.33%	NA
All Japonica	1512	78.00%	0.10%	1.26%	20.70%	NA
Aus	269	15.60%	0.70%	25.65%	57.99%	NA
Indica I	595	4.70%	0.50%	5.88%	88.91%	NA
Indica II	465	35.90%	0.60%	7.74%	55.70%	NA
Indica III	913	10.10%	0.30%	5.59%	84.01%	NA
Indica Intermediate	786	20.50%	0.50%	8.91%	70.10%	NA
Temperate Japonica	767	88.80%	0.00%	0.52%	10.69%	NA
Tropical Japonica	504	62.50%	0.20%	1.98%	35.32%	NA
Japonica Intermediate	241	75.90%	0.00%	2.07%	21.99%	NA
VI/Aromatic	96	34.40%	0.00%	14.58%	51.04%	NA
Intermediate	90	62.20%	0.00%	7.78%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216422805	C -> DEL	N	N	silent_mutation	Average:42.117; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N
vg1216422805	C -> A	LOC_Os12g27860.1	upstream_gene_variant ; 90.0bp to feature; MODIFIER	silent_mutation	Average:42.117; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N
vg1216422805	C -> A	LOC_Os12g27850-LOC_Os12g27860	intergenic_region ; MODIFIER	silent_mutation	Average:42.117; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216422805	2.46E-06	2.46E-06	mr1048_2	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
vg1216422805	NA	1.19E-06	mr1057_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
vg1216422805	NA	1.02E-06	mr1123_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
vg1216422805	NA	8.68E-08	mr1242_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
vg1216422805	9.10E-06	NA	mr1258_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
vg1216422805	2.68E-06	NA	mr1258_2	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
vg1216422805	NA	3.86E-06	mr1570_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
vg1216422805	NA	4.85E-06	mr1574_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