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Detailed information for vg0412900448:

Variant ID: vg0412900448 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12900448
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACCCAACCCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTAGTTGTTAAGCAGGTTTTATGAATTAAAACACTAACTTGGG[T/C]
ACATTGCTCGGCTTGCCCATAACCGAGGGCGCGGCTATTCGAATAGATTATACTCTGATCAGAGGTGTACATCTTTACCCACAAGACACATCTTCCTCAC

Reverse complement sequence

GTGAGGAAGATGTGTCTTGTGGGTAAAGATGTACACCTCTGATCAGAGTATAATCTATTCGAATAGCCGCGCCCTCGGTTATGGGCAAGCCGAGCAATGT[A/G]
CCCAAGTTAGTGTTTTAATTCATAAAACCTGCTTAACAACTAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGGTTGGGTTG

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	86.90%	0.40%	10.18%	2.48%	NA
All Indica	2759	79.30%	0.60%	16.35%	3.73%	NA
All Japonica	1512	99.20%	0.00%	0.40%	0.40%	NA
Aus	269	91.80%	0.70%	5.95%	1.49%	NA
Indica I	595	77.80%	0.80%	17.98%	3.36%	NA
Indica II	465	76.80%	0.00%	15.48%	7.74%	NA
Indica III	913	81.50%	0.10%	17.20%	1.20%	NA
Indica Intermediate	786	79.40%	1.40%	14.63%	4.58%	NA
Temperate Japonica	767	99.30%	0.00%	0.39%	0.26%	NA
Tropical Japonica	504	99.40%	0.00%	0.40%	0.20%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	0.00%	8.89%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412900448	T -> C	LOC_Os04g22770.1	upstream_gene_variant ; 1560.0bp to feature; MODIFIER	silent_mutation	Average:23.271; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N
vg0412900448	T -> C	LOC_Os04g22780.1	upstream_gene_variant ; 1462.0bp to feature; MODIFIER	silent_mutation	Average:23.271; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N
vg0412900448	T -> C	LOC_Os04g22760.1	downstream_gene_variant ; 3042.0bp to feature; MODIFIER	silent_mutation	Average:23.271; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N
vg0412900448	T -> C	LOC_Os04g22790.1	downstream_gene_variant ; 2423.0bp to feature; MODIFIER	silent_mutation	Average:23.271; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N
vg0412900448	T -> C	LOC_Os04g22770-LOC_Os04g22780	intergenic_region ; MODIFIER	silent_mutation	Average:23.271; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N
vg0412900448	T -> DEL	N	N	silent_mutation	Average:23.271; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412900448	4.41E-06	NA	mr1519_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
vg0412900448	4.71E-08	2.87E-11	mr1519_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