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Detailed information for vg1202743490:

Variant ID: vg1202743490 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 2743490
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.11, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTTGAACTTCGTTAACAAATATTGTGTGTTCATGTGCCGTCATCTGGCATGTCTTAGGTGATCAATGACTGAAGTGATCGAGAGAGTTAGCTGTCGTT[T/C]
CGCTATATCAACTAACTTTTGTAACACCTTCTAGTAGAACTATATGTATTCTATATGAGTATTTGGCATTTTCCACCATTGTGTGGGTATGCCATATTTT

Reverse complement sequence

AAAATATGGCATACCCACACAATGGTGGAAAATGCCAAATACTCATATAGAATACATATAGTTCTACTAGAAGGTGTTACAAAAGTTAGTTGATATAGCG[A/G]
AACGACAGCTAACTCTCTCGATCACTTCAGTCATTGATCACCTAAGACATGCCAGATGACGGCACATGAACACACAATATTTGTTAACGAAGTTCAAACG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.50%	6.50%	0.28%	2.77%	NA
All Indica	2759	92.30%	6.80%	0.04%	0.87%	NA
All Japonica	1512	98.50%	1.30%	0.07%	0.13%	NA
Aus	269	22.70%	34.60%	4.09%	38.66%	NA
Indica I	595	94.10%	5.70%	0.00%	0.17%	NA
Indica II	465	98.30%	1.10%	0.00%	0.65%	NA
Indica III	913	88.80%	10.60%	0.00%	0.55%	NA
Indica Intermediate	786	91.30%	6.60%	0.13%	1.91%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	0.80%	0.00%	0.20%	NA
Japonica Intermediate	241	94.20%	5.00%	0.41%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1202743490	T -> C	LOC_Os12g05940.1	downstream_gene_variant ; 3379.0bp to feature; MODIFIER	silent_mutation	Average:55.811; most accessible tissue: Zhenshan97 root, score: 79.185	N	N	N	N
vg1202743490	T -> C	LOC_Os12g05950.1	downstream_gene_variant ; 2066.0bp to feature; MODIFIER	silent_mutation	Average:55.811; most accessible tissue: Zhenshan97 root, score: 79.185	N	N	N	N
vg1202743490	T -> C	LOC_Os12g05960.1	downstream_gene_variant ; 814.0bp to feature; MODIFIER	silent_mutation	Average:55.811; most accessible tissue: Zhenshan97 root, score: 79.185	N	N	N	N
vg1202743490	T -> C	LOC_Os12g05970.1	downstream_gene_variant ; 4085.0bp to feature; MODIFIER	silent_mutation	Average:55.811; most accessible tissue: Zhenshan97 root, score: 79.185	N	N	N	N
vg1202743490	T -> C	LOC_Os12g05950-LOC_Os12g05960	intergenic_region ; MODIFIER	silent_mutation	Average:55.811; most accessible tissue: Zhenshan97 root, score: 79.185	N	N	N	N
vg1202743490	T -> DEL	N	N	silent_mutation	Average:55.811; most accessible tissue: Zhenshan97 root, score: 79.185	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1202743490	3.02E-06	NA	mr1125_2	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