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Detailed information for vg0303248763:

Variant ID: vg0303248763 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 3248763
Reference Allele: GCCCAGCGGGCGCGGGTATA	Alternative Allele: ACCCAGCGGGCGCGGGTATA,G
Primary Allele: GCCCAGCGGGCGCGGGTATA	Secondary Allele: ACCCAGCGGGCGCGGGTATA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCACGGGTAGAGCAAAACCATGCCCGACCCGATGCCCGACTTTGCCCGCCCAAACCCTACCCACTAGAGTTAGCGGGCAAAACTCCGTGCCCGTACCCAT[GCCCAGCGGGCGCGGGTATA/ACCCAGCGGGCGCGGGTATA,G]
TCCGGCGGGTACCCAATGGATCTCACTTGAATAATAACTTGAAAGATATGTAATTTAACAAAGAGAAATAAAATAAAAAATTTATGAAATTATTGGTTAT

Reverse complement sequence

ATAACCAATAATTTCATAAATTTTTTATTTTATTTCTCTTTGTTAAATTACATATCTTTCAAGTTATTATTCAAGTGAGATCCATTGGGTACCCGCCGGA[TATACCCGCGCCCGCTGGGC/TATACCCGCGCCCGCTGGGT,C]
ATGGGTACGGGCACGGAGTTTTGCCCGCTAACTCTAGTGGGTAGGGTTTGGGCGGGCAAAGTCGGGCATCGGGTCGGGCATGGTTTTGCTCTACCCGTGC

Allele Frequencies:

Populations	Population Size	Frequency of GCCCAGCGGGCGCGGGTATA(primary allele)	Frequency of ACCCAGCGGGCGCGGGTATA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.40%	40.70%	4.63%	4.23%	NA
All Indica	2759	26.20%	59.30%	7.43%	7.10%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	15.20%	80.70%	3.72%	0.37%	NA
Indica I	595	34.50%	58.50%	6.55%	0.50%	NA
Indica II	465	13.50%	65.60%	9.89%	10.97%	NA
Indica III	913	23.00%	57.80%	8.32%	10.84%	NA
Indica Intermediate	786	31.20%	57.80%	5.60%	5.47%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	58.30%	39.60%	2.08%	0.00%	NA
Intermediate	90	60.00%	34.40%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0303248763	GCCCAGCGGGCGCGGGTATA -> ACCCAGCGGGCGCGGGTATA	LOC_Os03g06490.1	upstream_gene_variant ; 4224.0bp to feature; MODIFIER	silent_mutation	Average:46.279; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg0303248763	GCCCAGCGGGCGCGGGTATA -> ACCCAGCGGGCGCGGGTATA	LOC_Os03g06480-LOC_Os03g06490	intergenic_region ; MODIFIER	silent_mutation	Average:46.279; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg0303248763	GCCCAGCGGGCGCGGGTATA -> DEL	N	N	silent_mutation	Average:46.279; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg0303248763	GCCCAGCGGGCGCGGGTATA -> G	LOC_Os03g06490.1	upstream_gene_variant ; 4223.0bp to feature; MODIFIER	N	Average:46.279; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg0303248763	GCCCAGCGGGCGCGGGTATA -> G	LOC_Os03g06480-LOC_Os03g06490	intergenic_region ; MODIFIER	N	Average:46.279; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0303248763	NA	7.69E-06	mr1042	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
vg0303248763	4.40E-07	4.40E-07	mr1966	Ind_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
vg0303248763	NA	1.43E-16	mr1114_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
vg0303248763	NA	2.72E-06	mr1115_2	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
vg0303248763	NA	2.97E-07	mr1583_2	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