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Detailed information for vg0116844307:

Variant ID: vg0116844307 (JBrowse)	Variation Type: INDEL
Chromosome: chr01	Position: 16844307
Reference Allele: GAA	Alternative Allele: AAA,G
Primary Allele: GAA	Secondary Allele: AAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCTTCTCTATCACAAGGAACAGCAAGTAAATCAACTTGTGACAAAGGCATCTCAGCAATTGGTTCCACTAATAGTTGCTCTTCTCTAGCATGACAAGTG[GAA/AAA,G]
AAATGAAATTCATCAGAAGCATACTCATCTTGAGTAATTTCTGCACCATTTAATTTACCTTTTATGCCCTCTTCAGATAATGTAGGTGCATCAGCCTTCT

Reverse complement sequence

AGAAGGCTGATGCACCTACATTATCTGAAGAGGGCATAAAAGGTAAATTAAATGGTGCAGAAATTACTCAAGATGAGTATGCTTCTGATGAATTTCATTT[TTC/TTT,C]
CACTTGTCATGCTAGAGAAGAGCAACTATTAGTGGAACCAATTGCTGAGATGCCTTTGTCACAAGTTGATTTACTTGCTGTTCCTTGTGATAGAGAAGAG

Allele Frequencies:

Populations	Population Size	Frequency of GAA(primary allele)	Frequency of AAA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.40%	44.20%	0.38%	0.00%	NA
All Indica	2759	30.30%	69.20%	0.51%	0.00%	NA
All Japonica	1512	98.10%	1.90%	0.00%	0.00%	NA
Aus	269	53.20%	45.40%	1.49%	0.00%	NA
Indica I	595	54.60%	44.70%	0.67%	0.00%	NA
Indica II	465	39.40%	60.40%	0.22%	0.00%	NA
Indica III	913	4.30%	95.40%	0.33%	0.00%	NA
Indica Intermediate	786	36.90%	62.30%	0.76%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	95.40%	4.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0116844307	GAA -> G	LOC_Os01g29910.1	downstream_gene_variant ; 823.0bp to feature; MODIFIER	N	Average:9.418; most accessible tissue: Callus, score: 13.315	N	N	N	N
vg0116844307	GAA -> G	LOC_Os01g29910-LOC_Os01g30936	intergenic_region ; MODIFIER	N	Average:9.418; most accessible tissue: Callus, score: 13.315	N	N	N	N
vg0116844307	GAA -> AAA	LOC_Os01g29910.1	downstream_gene_variant ; 822.0bp to feature; MODIFIER	silent_mutation	Average:9.418; most accessible tissue: Callus, score: 13.315	N	N	N	N
vg0116844307	GAA -> AAA	LOC_Os01g29910-LOC_Os01g30936	intergenic_region ; MODIFIER	silent_mutation	Average:9.418; most accessible tissue: Callus, score: 13.315	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0116844307	NA	5.62E-08	mr1514	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
vg0116844307	4.39E-06	NA	mr1711	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
vg0116844307	NA	2.58E-07	mr1711	Ind_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