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Detailed information for vg0224854719:

Variant ID: vg0224854719 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24854719
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAAGATCTCTTTGCAGTGAGTTATGGTGGGTTATAAATGGTCTTGCTTCAGCACCACCTGCTGCTCCCTGTTTAGCCCGGTTGGAAAAAAAAAGAAAAA[T/G]
GACCAGACGATATTAATGATGACCAATAACAGTCAAATAATACAAAACAAACACTGGGGCACTGGGCAAGTCCATTTTACCACCCCCCCCCCCCCACCCA

Reverse complement sequence

TGGGTGGGGGGGGGGGGGTGGTAAAATGGACTTGCCCAGTGCCCCAGTGTTTGTTTTGTATTATTTGACTGTTATTGGTCATCATTAATATCGTCTGGTC[A/C]
TTTTTCTTTTTTTTTCCAACCGGGCTAAACAGGGAGCAGCAGGTGGTGCTGAAGCAAGACCATTTATAACCCACCATAACTCACTGCAAAGAGATCTTTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.30%	30.60%	0.08%	0.00%	NA
All Indica	2759	93.90%	5.90%	0.14%	0.00%	NA
All Japonica	1512	20.10%	79.90%	0.00%	0.00%	NA
Aus	269	88.10%	11.90%	0.00%	0.00%	NA
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	98.50%	1.30%	0.22%	0.00%	NA
Indica III	913	92.90%	7.10%	0.00%	0.00%	NA
Indica Intermediate	786	89.80%	9.80%	0.38%	0.00%	NA
Temperate Japonica	767	27.00%	73.00%	0.00%	0.00%	NA
Tropical Japonica	504	10.10%	89.90%	0.00%	0.00%	NA
Japonica Intermediate	241	19.10%	80.90%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	56.70%	43.30%	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
vg0224854719	T -> G	LOC_Os02g41470.1	intron_variant ; MODIFIER	silent_mutation	Average:54.717; most accessible tissue: Callus, score: 80.215	N	N	N	N
vg0224854719	T -> G	LOC_Os02g41470.2	intron_variant ; MODIFIER	silent_mutation	Average:54.717; most accessible tissue: Callus, score: 80.215	N	N	N	N
vg0224854719	T -> G	LOC_Os02g41470.3	intron_variant ; MODIFIER	silent_mutation	Average:54.717; most accessible tissue: Callus, score: 80.215	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224854719	3.62E-06	3.62E-06	mr1198	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
vg0224854719	NA	4.24E-10	mr1379	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
vg0224854719	NA	2.12E-06	mr1606	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