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Detailed information for vg0215723095:

Variant ID: vg0215723095 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 15723095
Reference Allele: C	Alternative Allele: CATGGCAAGACAACAA,T
Primary Allele: C	Secondary Allele: CATGGCAAGACAACAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAGTCGCTGGAGCAATCTTGTTCATCGCCAGAAGGTACTGCCGCCGTTTCAGTATTCTGCAACGGCCGTGTGTTTCCTGTTACAGGTAAATCGATGTGT[C/CATGGCAAGACAACAA,T]
GTAAATTGTTTGAAGTGATACTGTGTAATTTGTTTTATATATTGAGATTATTGTTATTTTTTTGGCAGAATCATGATGGTTGATGAGATGGCAGACAATT

Reverse complement sequence

AATTGTCTGCCATCTCATCAACCATCATGATTCTGCCAAAAAAATAACAATAATCTCAATATATAAAACAAATTACACAGTATCACTTCAAACAATTTAC[G/TTGTTGTCTTGCCATG,A]
ACACATCGATTTACCTGTAACAGGAAACACACGGCCGTTGCAGAATACTGAAACGGCGGCAGTACCTTCTGGCGATGAACAAGATTGCTCCAGCGACTCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of CATGGCAAGACAACAA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.90%	4.40%	2.58%	15.21%	T: 3.91%
All Indica	2759	80.50%	0.80%	1.74%	16.56%	T: 0.43%
All Japonica	1512	74.70%	0.30%	2.58%	15.08%	T: 7.34%
Aus	269	24.90%	63.90%	5.20%	5.58%	T: 0.37%
Indica I	595	79.80%	0.50%	1.85%	17.82%	NA
Indica II	465	83.90%	0.00%	1.94%	13.33%	T: 0.86%
Indica III	913	79.50%	0.70%	1.53%	17.63%	T: 0.66%
Indica Intermediate	786	80.00%	1.70%	1.78%	16.28%	T: 0.25%
Temperate Japonica	767	93.10%	0.00%	0.91%	1.56%	T: 4.43%
Tropical Japonica	504	56.20%	0.80%	3.37%	36.31%	T: 3.37%
Japonica Intermediate	241	54.80%	0.40%	6.22%	13.69%	T: 24.90%
VI/Aromatic	96	21.90%	2.10%	15.62%	3.12%	T: 57.29%
Intermediate	90	63.30%	5.60%	6.67%	17.78%	T: 6.67%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0215723095	C -> T	LOC_Os02g26770.1	upstream_gene_variant ; 4238.0bp to feature; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> T	LOC_Os02g26780.1	upstream_gene_variant ; 88.0bp to feature; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> T	LOC_Os02g26790.1	downstream_gene_variant ; 2586.0bp to feature; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> T	LOC_Os02g26794.1	downstream_gene_variant ; 3671.0bp to feature; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> T	LOC_Os02g26770-LOC_Os02g26780	intergenic_region ; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> DEL	N	N	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> CATGGCAAGACAACAA	LOC_Os02g26770.1	upstream_gene_variant ; 4239.0bp to feature; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> CATGGCAAGACAACAA	LOC_Os02g26780.1	upstream_gene_variant ; 87.0bp to feature; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> CATGGCAAGACAACAA	LOC_Os02g26790.1	downstream_gene_variant ; 2585.0bp to feature; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> CATGGCAAGACAACAA	LOC_Os02g26794.1	downstream_gene_variant ; 3670.0bp to feature; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0215723095	C -> CATGGCAAGACAACAA	LOC_Os02g26770-LOC_Os02g26780	intergenic_region ; MODIFIER	silent_mutation	Average:68.256; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0215723095	5.75E-07	5.75E-07	mr1343	Jap_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
vg0215723095	NA	1.88E-07	mr1354	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
vg0215723095	NA	2.28E-06	mr1549_2	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