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Detailed information for vg1004721522:

Variant ID: vg1004721522 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4721522
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCGGAAGCTGGTTGGCGGAATTGTATACGGCAAGGATTGTGTGTTTGCATGGCGTCCCTAAGAAAATAGTGTCTGATCGAGGTAGTTAGTTTACTTCAA[A/T]
GTTTTGGAAGAAACTTCAAGAAGAGATGGGTTCTAAGCTAAACTTTAGTACTACTTATCATCCACAGACAGACGGACAAACCAAAAGGGTAAATCAGATT

Reverse complement sequence

AATCTGATTTACCCTTTTGGTTTGTCCGTCTGTCTGTGGATGATAAGTAGTACTAAAGTTTAGCTTAGAACCCATCTCTTCTTGAAGTTTCTTCCAAAAC[T/A]
TTGAAGTAAACTAACTACCTCGATCAGACACTATTTTCTTAGGGACGCCATGCAAACACACAATCCTTGCCGTATACAATTCCGCCAACCAGCTTCCGGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.70%	5.20%	9.97%	18.15%	NA
All Indica	2759	60.40%	8.70%	11.82%	19.06%	NA
All Japonica	1512	86.90%	0.10%	4.50%	8.47%	NA
Aus	269	9.70%	0.40%	19.70%	70.26%	NA
Indica I	595	32.80%	17.00%	15.80%	34.45%	NA
Indica II	465	59.60%	8.40%	11.40%	20.65%	NA
Indica III	913	76.20%	4.90%	9.31%	9.53%	NA
Indica Intermediate	786	63.50%	7.00%	11.96%	17.56%	NA
Temperate Japonica	767	91.70%	0.10%	1.56%	6.65%	NA
Tropical Japonica	504	84.70%	0.00%	9.33%	5.95%	NA
Japonica Intermediate	241	76.30%	0.40%	3.73%	19.50%	NA
VI/Aromatic	96	86.50%	0.00%	12.50%	1.04%	NA
Intermediate	90	68.90%	2.20%	13.33%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004721522	A -> T	LOC_Os10g08710.1	upstream_gene_variant ; 3849.0bp to feature; MODIFIER	silent_mutation	Average:13.272; most accessible tissue: Callus, score: 33.34	N	N	N	N
vg1004721522	A -> T	LOC_Os10g08696.1	downstream_gene_variant ; 3838.0bp to feature; MODIFIER	silent_mutation	Average:13.272; most accessible tissue: Callus, score: 33.34	N	N	N	N
vg1004721522	A -> T	LOC_Os10g08702.1	intron_variant ; MODIFIER	silent_mutation	Average:13.272; most accessible tissue: Callus, score: 33.34	N	N	N	N
vg1004721522	A -> DEL	N	N	silent_mutation	Average:13.272; most accessible tissue: Callus, score: 33.34	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004721522	1.30E-06	9.92E-07	mr1520	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