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Detailed information for vg0203808446:

Variant ID: vg0203808446 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 3808446
Reference Allele: C	Alternative Allele: T,CGA,CAA
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAGACCTACCCCCCTTACAGTGGGTAGTCTTACTTTCGCCTGACTGAGAACCTTTGAACTGTTGTCCTTGAAAAAATGACCAACATTTCTCGGATTTA[C/T,CGA,CAA]
AGATGCCCTGACTTTGAAGACTAAAACTTCATCGGTCCATCAAATTGAAGCAATGGCGATGCACTTTCATCCCGACAAGATTTGGAACTTAAGCCTTAGT

Reverse complement sequence

ACTAAGGCTTAAGTTCCAAATCTTGTCGGGATGAAAGTGCATCGCCATTGCTTCAATTTGATGGACCGATGAAGTTTTAGTCTTCAAAGTCAGGGCATCT[G/A,TCG,TTG]
TAAATCCGAGAAATGTTGGTCATTTTTTCAAGGACAACAGTTCAAAGGTTCTCAGTCAGGCGAAAGTAAGACTACCCACTGTAAGGGGGGTAGGTCTCGG

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	64.10%	9.30%	3.64%	21.63%	CGA: 1.29%; CAA: 0.08%
All Indica	2759	68.90%	15.50%	5.69%	7.79%	CGA: 1.99%; CAA: 0.11%
All Japonica	1512	56.70%	0.20%	0.13%	42.99%	NA
Aus	269	41.60%	0.00%	3.35%	53.16%	CGA: 1.49%; CAA: 0.37%
Indica I	595	78.20%	6.20%	5.71%	5.71%	CGA: 4.03%; CAA: 0.17%
Indica II	465	64.50%	4.30%	11.18%	16.56%	CGA: 3.23%; CAA: 0.22%
Indica III	913	62.00%	29.50%	2.74%	5.70%	CGA: 0.11%
Indica Intermediate	786	72.50%	13.00%	5.85%	6.62%	CGA: 1.91%; CAA: 0.13%
Temperate Japonica	767	71.10%	0.00%	0.00%	28.94%	NA
Tropical Japonica	504	43.10%	0.40%	0.20%	56.35%	NA
Japonica Intermediate	241	39.40%	0.40%	0.41%	59.75%	NA
VI/Aromatic	96	89.60%	3.10%	1.04%	6.25%	NA
Intermediate	90	80.00%	5.60%	3.33%	8.89%	CGA: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203808446	C -> T	LOC_Os02g07380.1	upstream_gene_variant ; 2811.0bp to feature; MODIFIER	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0203808446	C -> T	LOC_Os02g07370.1	downstream_gene_variant ; 1907.0bp to feature; MODIFIER	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0203808446	C -> T	LOC_Os02g07370-LOC_Os02g07380	intergenic_region ; MODIFIER	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0203808446	C -> DEL	N	N	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0203808446	C -> CGA	LOC_Os02g07380.1	upstream_gene_variant ; 2810.0bp to feature; MODIFIER	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0203808446	C -> CGA	LOC_Os02g07370.1	downstream_gene_variant ; 1908.0bp to feature; MODIFIER	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0203808446	C -> CGA	LOC_Os02g07370-LOC_Os02g07380	intergenic_region ; MODIFIER	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0203808446	C -> CAA	LOC_Os02g07380.1	upstream_gene_variant ; 2810.0bp to feature; MODIFIER	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0203808446	C -> CAA	LOC_Os02g07370.1	downstream_gene_variant ; 1908.0bp to feature; MODIFIER	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0203808446	C -> CAA	LOC_Os02g07370-LOC_Os02g07380	intergenic_region ; MODIFIER	silent_mutation	Average:28.499; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203808446	4.10E-06	4.10E-06	mr1499	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