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Detailed information for vg0505704465:

Variant ID: vg0505704465 (JBrowse)	Variation Type: INDEL
Chromosome: chr05	Position: 5704465
Reference Allele: ACAT	Alternative Allele: GCAT,A
Primary Allele: GCAT	Secondary Allele: ACAT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGTATAGGTATGATTTTATATTTTAATTAATTACATAATGTAAATTTTTCTTAACCTTTTCTTTAATTTCTCATGTTTTCTCCCGTTGCAACGCACGG[ACAT/GCAT,A]
TTTTTCTAGTAAAGAAAAAAAAACATCCGGAACCATCATATACGGAACCAACGTACGTAATGTCGAACGTACGTGCGTATGTACTGTACGCACTTCCCTT

Reverse complement sequence

AAGGGAAGTGCGTACAGTACATACGCACGTACGTTCGACATTACGTACGTTGGTTCCGTATATGATGGTTCCGGATGTTTTTTTTTCTTTACTAGAAAAA[ATGT/ATGC,T]
CCGTGCGTTGCAACGGGAGAAAACATGAGAAATTAAAGAAAAGGTTAAGAAAAATTTACATTATGTAATTAATTAAAATATAAAATCATACCTATACATG

Allele Frequencies:

Populations	Population Size	Frequency of GCAT(primary allele)	Frequency of ACAT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.50%	11.90%	24.52%	32.01%	A: 0.06%
All Indica	2759	31.30%	2.20%	34.43%	31.97%	A: 0.11%
All Japonica	1512	26.50%	31.90%	4.10%	37.50%	NA
Aus	269	43.10%	0.00%	42.75%	14.13%	NA
Indica I	595	26.70%	5.90%	43.87%	23.53%	NA
Indica II	465	26.00%	1.10%	37.63%	35.27%	NA
Indica III	913	36.50%	0.20%	26.07%	37.02%	A: 0.22%
Indica Intermediate	786	31.80%	2.40%	35.11%	30.53%	A: 0.13%
Temperate Japonica	767	36.10%	53.70%	3.39%	6.78%	NA
Tropical Japonica	504	10.10%	5.40%	5.16%	79.37%	NA
Japonica Intermediate	241	30.30%	17.80%	4.15%	47.72%	NA
VI/Aromatic	96	79.20%	6.20%	11.46%	3.12%	NA
Intermediate	90	34.40%	16.70%	23.33%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0505704465	ACAT -> DEL	N	N	silent_mutation	Average:13.219; most accessible tissue: Callus, score: 63.196	N	N	N	N
vg0505704465	ACAT -> GCAT	LOC_Os05g10480.1	upstream_gene_variant ; 4993.0bp to feature; MODIFIER	silent_mutation	Average:13.219; most accessible tissue: Callus, score: 63.196	N	N	N	N
vg0505704465	ACAT -> GCAT	LOC_Os05g10490.1	upstream_gene_variant ; 3574.0bp to feature; MODIFIER	silent_mutation	Average:13.219; most accessible tissue: Callus, score: 63.196	N	N	N	N
vg0505704465	ACAT -> GCAT	LOC_Os05g10480-LOC_Os05g10490	intergenic_region ; MODIFIER	silent_mutation	Average:13.219; most accessible tissue: Callus, score: 63.196	N	N	N	N
vg0505704465	ACAT -> A	LOC_Os05g10480.1	upstream_gene_variant ; 4994.0bp to feature; MODIFIER	silent_mutation	Average:13.219; most accessible tissue: Callus, score: 63.196	N	N	N	N
vg0505704465	ACAT -> A	LOC_Os05g10490.1	upstream_gene_variant ; 3573.0bp to feature; MODIFIER	silent_mutation	Average:13.219; most accessible tissue: Callus, score: 63.196	N	N	N	N
vg0505704465	ACAT -> A	LOC_Os05g10480-LOC_Os05g10490	intergenic_region ; MODIFIER	silent_mutation	Average:13.219; most accessible tissue: Callus, score: 63.196	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505704465	NA	4.78E-11	Heading_date	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0505704465	NA	3.96E-10	Heading_date	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0505704465	4.13E-06	7.02E-08	mr1791	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
vg0505704465	NA	4.76E-09	mr1588_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