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Detailed information for vg0224549820:

Variant ID: vg0224549820 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24549820
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCTCTAGTCATGATACTCCCGGTCCCATATCACCGACACAAGCAATAACAAGATAAAAGTAATCTGAATTGCAAATAAGAATTAAATACGAATGATAAG[T/C]
TGGGGTTCCGAAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTATCAAAACCCAATAAACTG

Reverse complement sequence

CAGTTTATTGGGTTTTGATAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTTCGGAACCCCA[A/G]
CTTATCATTCGTATTTAATTCTTATTTGCAATTCAGATTACTTTTATCTTGTTATTGCTTGTGTCGGTGATATGGGACCGGGAGTATCATGACTAGAGGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	9.60%	4.80%	2.12%	83.45%	NA
All Indica	2759	4.60%	0.80%	1.38%	93.22%	NA
All Japonica	1512	19.20%	13.30%	3.64%	63.82%	NA
Aus	269	8.90%	0.00%	0.37%	90.71%	NA
Indica I	595	1.20%	0.50%	0.34%	97.98%	NA
Indica II	465	4.70%	0.40%	0.65%	94.19%	NA
Indica III	913	5.60%	0.30%	2.30%	91.79%	NA
Indica Intermediate	786	6.10%	1.70%	1.53%	90.71%	NA
Temperate Japonica	767	22.40%	16.80%	3.39%	57.37%	NA
Tropical Japonica	504	15.30%	3.40%	1.79%	79.56%	NA
Japonica Intermediate	241	17.40%	22.80%	8.30%	51.45%	NA
VI/Aromatic	96	1.00%	1.00%	1.04%	96.88%	NA
Intermediate	90	12.20%	4.40%	5.56%	77.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224549820	T -> DEL	N	N	silent_mutation	Average:16.532; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0224549820	T -> C	LOC_Os02g40480.1	upstream_gene_variant ; 1232.0bp to feature; MODIFIER	silent_mutation	Average:16.532; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0224549820	T -> C	LOC_Os02g40480-LOC_Os02g40490	intergenic_region ; MODIFIER	silent_mutation	Average:16.532; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224549820	4.45E-06	4.45E-06	mr1910	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