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Detailed information for vg0816207802:

Variant ID: vg0816207802 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 16207802
Reference Allele: A	Alternative Allele: ATGT
Primary Allele: A	Secondary Allele: ATGT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATGCTTGATTTATATCTTGAAGAAATTCATTCTACACTAACGTTTACTCAGGGACGAGCAAAGGGCTAAGTGTGGGGGGTTTTGTTGGCGGCTGTTAA[A/ATGT]
TGCCAATTCTATACCGCCAACATCTGCATAAAGTTCAGATAATAAAACATCCAACATAGTGATAGGTGCTTAATCTCACATATTCCAAAGTGTTGGTGTA

Reverse complement sequence

TACACCAACACTTTGGAATATGTGAGATTAAGCACCTATCACTATGTTGGATGTTTTATTATCTGAACTTTATGCAGATGTTGGCGGTATAGAATTGGCA[T/ACAT]
TTAACAGCCGCCAACAAAACCCCCCACACTTAGCCCTTTGCTCGTCCCTGAGTAAACGTTAGTGTAGAATGAATTTCTTCAAGATATAAATCAAGCATAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of ATGT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.80%	0.10%	0.87%	10.26%	NA
All Indica	2759	88.40%	0.10%	1.05%	10.37%	NA
All Japonica	1512	89.40%	0.00%	0.53%	10.12%	NA
Aus	269	85.10%	0.00%	1.12%	13.75%	NA
Indica I	595	86.20%	0.00%	1.34%	12.44%	NA
Indica II	465	89.20%	0.00%	1.29%	9.46%	NA
Indica III	913	88.40%	0.30%	1.31%	9.97%	NA
Indica Intermediate	786	89.70%	0.10%	0.38%	9.80%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	73.60%	0.00%	1.39%	25.00%	NA
Japonica Intermediate	241	90.50%	0.00%	0.41%	9.13%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	91.10%	0.00%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816207802	A -> ATGT	LOC_Os08g26670.1	upstream_gene_variant ; 2081.0bp to feature; MODIFIER	silent_mutation	Average:24.891; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0816207802	A -> ATGT	LOC_Os08g26650.1	downstream_gene_variant ; 4583.0bp to feature; MODIFIER	silent_mutation	Average:24.891; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0816207802	A -> ATGT	LOC_Os08g26660.1	downstream_gene_variant ; 1686.0bp to feature; MODIFIER	silent_mutation	Average:24.891; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0816207802	A -> ATGT	LOC_Os08g26680.1	downstream_gene_variant ; 4915.0bp to feature; MODIFIER	silent_mutation	Average:24.891; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0816207802	A -> ATGT	LOC_Os08g26660-LOC_Os08g26670	intergenic_region ; MODIFIER	silent_mutation	Average:24.891; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0816207802	A -> DEL	N	N	silent_mutation	Average:24.891; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816207802	NA	8.21E-06	mr1076	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
vg0816207802	NA	2.69E-06	mr1082	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
vg0816207802	NA	4.71E-06	mr1083	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
vg0816207802	NA	4.06E-06	mr1408	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
vg0816207802	1.13E-07	1.22E-09	mr1082_2	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
vg0816207802	7.87E-07	3.55E-08	mr1083_2	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
vg0816207802	5.93E-06	NA	mr1103_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
vg0816207802	NA	2.08E-06	mr1226_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