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Detailed information for vg0815289622:

Variant ID: vg0815289622 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 15289622
Reference Allele: TA	Alternative Allele: CA,TATCCAAAATTCCAA,T
Primary Allele: TA	Secondary Allele: CA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAATTCTAAATTTATTTTTTTTGATAGAGAGAGTATGCAGGATTCTATTGTATCATAGTCCTAGGCTGGGTTCGTTGTTGTGTGTTGGGAATACATTTC[TA/CA,TATCCAAAATTCCAA,T]
GCGCACGAAAAATTGAGCGGTCCATTAGCATGTGATTAATTCAGTATTAGGTAATTTTATTTTCAAAAATGGATCAATATGATTTTTTAAGCAACTTTCA

Reverse complement sequence

TGAAAGTTGCTTAAAAAATCATATTGATCCATTTTTGAAAATAAAATTACCTAATACTGAATTAATCACATGCTAATGGACCGCTCAATTTTTCGTGCGC[TA/TG,TTGGAATTTTGGATA,A]
GAAATGTATTCCCAACACACAACAACGAACCCAGCCTAGGACTATGATACAATAGAATCCTGCATACTCTCTCTATCAAAAAAAATAAATTTAGAATTGG

Allele Frequencies:

Populations	Population Size	Frequency of TA(primary allele)	Frequency of CA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.40%	3.80%	11.19%	8.55%	TATCCAAAATTCCAA: 1.38%; T: 0.72%
All Indica	2759	64.20%	0.70%	17.87%	14.03%	TATCCAAAATTCCAA: 2.07%; T: 1.12%
All Japonica	1512	92.30%	7.10%	0.26%	0.20%	TATCCAAAATTCCAA: 0.07%
Aus	269	83.60%	0.00%	8.92%	4.46%	TATCCAAAATTCCAA: 1.86%; T: 1.12%
Indica I	595	62.40%	0.00%	25.71%	9.24%	T: 1.34%; TATCCAAAATTCCAA: 1.34%
Indica II	465	60.90%	3.20%	20.22%	12.90%	TATCCAAAATTCCAA: 1.94%; T: 0.86%
Indica III	913	67.00%	0.10%	10.08%	17.96%	TATCCAAAATTCCAA: 3.40%; T: 1.42%
Indica Intermediate	786	64.20%	0.50%	19.59%	13.74%	TATCCAAAATTCCAA: 1.15%; T: 0.76%
Temperate Japonica	767	91.30%	8.00%	0.39%	0.26%	TATCCAAAATTCCAA: 0.13%
Tropical Japonica	504	91.30%	8.30%	0.20%	0.20%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	60.40%	38.50%	0.00%	1.04%	NA
Intermediate	90	73.30%	14.40%	8.89%	1.11%	TATCCAAAATTCCAA: 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
vg0815289622	TA -> T	LOC_Os08g25160-LOC_Os08g25180	intergenic_region ; MODIFIER	silent_mutation	Average:55.983; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0815289622	TA -> TATCCAAAATTCCAA	LOC_Os08g25160-LOC_Os08g25180	intergenic_region ; MODIFIER	silent_mutation	Average:55.983; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0815289622	TA -> DEL	N	N	silent_mutation	Average:55.983; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0815289622	TA -> CA	LOC_Os08g25160-LOC_Os08g25180	intergenic_region ; MODIFIER	silent_mutation	Average:55.983; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0815289622	NA	4.78E-06	mr1155_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
vg0815289622	5.71E-06	NA	mr1408_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
vg0815289622	7.15E-07	NA	mr1771_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
vg0815289622	3.89E-06	NA	mr1784_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
vg0815289622	4.00E-06	NA	mr1862_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