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Detailed information for vg1213095961:

Variant ID: vg1213095961 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13095961
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: 327. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGTTAAACATGCACACATTATTTGCCAAAATCGCTGAACATGAACAGTATAAATGGTAACGTTGTGCACGTATCTTCGTACCAAAACATGTTAACTT[C/T]
TGAAGATGGTGATATAAATTAGATACTCCTACCTTCTTGTCTTTGGGGAAATCGATGGACTGCAGGTACGCCACATATGCGAACGACGAAGCGAAGATCT

Reverse complement sequence

AGATCTTCGCTTCGTCGTTCGCATATGTGGCGTACCTGCAGTCCATCGATTTCCCCAAAGACAAGAAGGTAGGAGTATCTAATTTATATCACCATCTTCA[G/A]
AAGTTAACATGTTTTGGTACGAAGATACGTGCACAACGTTACCATTTATACTGTTCATGTTCAGCGATTTTGGCAAATAATGTGTGCATGTTTAACATTT

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	79.80%	7.90%	0.38%	11.96%	NA
All Indica	2759	77.20%	3.30%	0.58%	18.99%	NA
All Japonica	1512	97.10%	0.30%	0.13%	2.51%	NA
Aus	269	23.00%	77.00%	0.00%	0.00%	NA
Indica I	595	97.60%	1.20%	0.17%	1.01%	NA
Indica II	465	53.80%	1.90%	1.08%	43.23%	NA
Indica III	913	77.50%	3.40%	0.22%	18.84%	NA
Indica Intermediate	786	75.10%	5.50%	1.02%	18.45%	NA
Temperate Japonica	767	95.30%	0.00%	0.26%	4.43%	NA
Tropical Japonica	504	99.40%	0.20%	0.00%	0.40%	NA
Japonica Intermediate	241	97.90%	1.20%	0.00%	0.83%	NA
VI/Aromatic	96	37.50%	62.50%	0.00%	0.00%	NA
Intermediate	90	84.40%	12.20%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213095961	C -> DEL	N	N	silent_mutation	Average:60.741; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N
vg1213095961	C -> T	LOC_Os12g23160.1	upstream_gene_variant ; 2887.0bp to feature; MODIFIER	silent_mutation	Average:60.741; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N
vg1213095961	C -> T	LOC_Os12g23170.1	upstream_gene_variant ; 3687.0bp to feature; MODIFIER	silent_mutation	Average:60.741; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N
vg1213095961	C -> T	LOC_Os12g23150.1	intron_variant ; MODIFIER	silent_mutation	Average:60.741; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213095961	NA	1.41E-06	mr1126_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
vg1213095961	NA	1.09E-09	mr1166_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