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Detailed information for vg1221738881:

Variant ID: vg1221738881 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21738881
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGAGATGGACGAGATTGTCCTCTGTTTCTTGTGGATATTGGTCGAGCATTGCGACGTTTACTCTCCGAGGGTCGATGAATCCAGTATCGAAAACCCTCT[A/G]
CCGTCGGGCCCTTTGAATCTCCATTCTACAACGATAAAAGGGAGTATATTATTTTCTATAGTCTACTTATATACAAGGACCTAATTAATTAAAGGAGACG

Reverse complement sequence

CGTCTCCTTTAATTAATTAGGTCCTTGTATATAAGTAGACTATAGAAAATAATATACTCCCTTTTATCGTTGTAGAATGGAGATTCAAAGGGCCCGACGG[T/C]
AGAGGGTTTTCGATACTGGATTCATCGACCCTCGGAGAGTAAACGTCGCAATGCTCGACCAATATCCACAAGAAACAGAGGACAATCTCGTCCATCTCCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.00%	9.80%	21.77%	23.38%	NA
All Indica	2759	52.60%	1.80%	21.57%	24.10%	NA
All Japonica	1512	41.30%	20.50%	24.93%	13.23%	NA
Aus	269	4.10%	9.30%	9.67%	76.95%	NA
Indica I	595	34.80%	0.50%	26.22%	38.49%	NA
Indica II	465	58.90%	3.00%	15.91%	22.15%	NA
Indica III	913	60.10%	1.80%	22.23%	15.88%	NA
Indica Intermediate	786	53.40%	2.00%	20.61%	23.92%	NA
Temperate Japonica	767	65.20%	6.50%	14.60%	13.69%	NA
Tropical Japonica	504	13.90%	45.60%	30.95%	9.52%	NA
Japonica Intermediate	241	22.80%	12.40%	45.23%	19.50%	NA
VI/Aromatic	96	3.10%	56.20%	19.79%	20.83%	NA
Intermediate	90	43.30%	28.90%	13.33%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221738881	A -> DEL	N	N	silent_mutation	Average:9.065; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1221738881	A -> G	LOC_Os12g35720.1	intron_variant ; MODIFIER	silent_mutation	Average:9.065; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221738881	7.84E-07	7.84E-07	mr1317	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