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Detailed information for vg0432620685:

Variant ID: vg0432620685 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 32620685
Reference Allele: CGA	Alternative Allele: TGA,C
Primary Allele: CGA	Secondary Allele: TGA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGCCAGACCACTTGCGTCGTCATGCGTCGATGTTCGTGTCATTTTCATGTAATGTTGAGCAATATAGATGGTATATTTATGCTAAAAAAAATTAAATTC[CGA/TGA,C]
GTAAAAAAATAAACTGTATATTTTTAAATTTAATTCGTTTGTACACTGCATATTGAACTAGGAAATGCTCGATTGTTCACCATGTCATAATATGATGCCC

Reverse complement sequence

GGGCATCATATTATGACATGGTGAACAATCGAGCATTTCCTAGTTCAATATGCAGTGTACAAACGAATTAAATTTAAAAATATACAGTTTATTTTTTTAC[TCG/TCA,G]
GAATTTAATTTTTTTTAGCATAAATATACCATCTATATTGCTCAACATTACATGAAAATGACACGAACATCGACGCATGACGACGCAAGTGGTCTGGCAC

Allele Frequencies:

Populations	Population Size	Frequency of CGA(primary allele)	Frequency of TGA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.60%	6.80%	0.32%	0.13%	C: 0.15%
All Indica	2759	94.00%	5.20%	0.40%	0.18%	C: 0.25%
All Japonica	1512	93.40%	6.50%	0.13%	0.00%	NA
Aus	269	77.70%	21.60%	0.37%	0.37%	NA
Indica I	595	96.60%	3.00%	0.34%	0.00%	NA
Indica II	465	98.70%	0.90%	0.22%	0.22%	NA
Indica III	913	89.30%	9.10%	0.55%	0.44%	C: 0.66%
Indica Intermediate	786	94.70%	4.80%	0.38%	0.00%	C: 0.13%
Temperate Japonica	767	92.20%	7.60%	0.26%	0.00%	NA
Tropical Japonica	504	94.80%	5.20%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.80%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	14.60%	1.04%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0432620685	CGA -> C	LOC_Os04g54840.1	downstream_gene_variant ; 1736.0bp to feature; MODIFIER	silent_mutation	Average:54.044; most accessible tissue: Callus, score: 85.824	N	N	N	N
vg0432620685	CGA -> C	LOC_Os04g54840-LOC_Os04g54850	intergenic_region ; MODIFIER	silent_mutation	Average:54.044; most accessible tissue: Callus, score: 85.824	N	N	N	N
vg0432620685	CGA -> DEL	N	N	silent_mutation	Average:54.044; most accessible tissue: Callus, score: 85.824	N	N	N	N
vg0432620685	CGA -> TGA	LOC_Os04g54840.1	downstream_gene_variant ; 1735.0bp to feature; MODIFIER	silent_mutation	Average:54.044; most accessible tissue: Callus, score: 85.824	N	N	N	N
vg0432620685	CGA -> TGA	LOC_Os04g54840-LOC_Os04g54850	intergenic_region ; MODIFIER	silent_mutation	Average:54.044; most accessible tissue: Callus, score: 85.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432620685	NA	5.02E-06	mr1441	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
vg0432620685	6.21E-06	NA	mr1855	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
vg0432620685	7.35E-10	7.35E-10	mr1855	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
vg0432620685	1.93E-06	5.64E-07	mr1962	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