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Detailed information for vg0224432425:

Variant ID: vg0224432425 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24432425
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCACTTGGAAAATTCTTGCTGTTGAAAGTCCCAAACCTTTGATGGGAGGTGAATGGATTTCAAAATTAATTCAGAGGCTGTAGACCACCCGTTAATATG[T/C]
GCTGCTCCCATATCATCCAGTGCTTGAAGCCTTGCACCAATATGTGGATTGAAAGAATTTAACACAAGACTTGATATATATTTATTCTTCAAAGTCTCAG

Reverse complement sequence

CTGAGACTTTGAAGAATAAATATATATCAAGTCTTGTGTTAAATTCTTTCAATCCACATATTGGTGCAAGGCTTCAAGCACTGGATGATATGGGAGCAGC[A/G]
CATATTAACGGGTGGTCTACAGCCTCTGAATTAATTTTGAAATCCATTCACCTCCCATCAAAGGTTTGGGACTTTCAACAGCAAGAATTTTCCAAGTGCA

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	70.50%	5.40%	1.54%	22.56%	NA
All Indica	2759	72.60%	6.70%	1.74%	18.96%	NA
All Japonica	1512	61.80%	4.10%	1.19%	32.87%	NA
Aus	269	85.90%	2.60%	2.23%	9.29%	NA
Indica I	595	51.60%	10.40%	4.03%	33.95%	NA
Indica II	465	94.60%	1.30%	0.65%	3.44%	NA
Indica III	913	67.70%	8.30%	1.64%	22.34%	NA
Indica Intermediate	786	81.00%	5.30%	0.76%	12.85%	NA
Temperate Japonica	767	52.20%	4.80%	1.17%	41.85%	NA
Tropical Japonica	504	81.00%	3.00%	0.40%	15.67%	NA
Japonica Intermediate	241	52.70%	4.10%	2.90%	40.25%	NA
VI/Aromatic	96	91.70%	1.00%	0.00%	7.29%	NA
Intermediate	90	83.30%	0.00%	1.11%	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
vg0224432425	T -> DEL	LOC_Os02g40340.2	N	frameshift_variant	Average:54.818; most accessible tissue: Callus, score: 82.255	N	N	N	N
vg0224432425	T -> DEL	LOC_Os02g40340.1	N	frameshift_variant	Average:54.818; most accessible tissue: Callus, score: 82.255	N	N	N	N
vg0224432425	T -> C	LOC_Os02g40340.1	synonymous_variant ; p.Ala302Ala; LOW	synonymous_codon	Average:54.818; most accessible tissue: Callus, score: 82.255	N	N	N	N
vg0224432425	T -> C	LOC_Os02g40340.2	synonymous_variant ; p.Ala302Ala; LOW	synonymous_codon	Average:54.818; most accessible tissue: Callus, score: 82.255	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224432425	9.26E-06	NA	mr1072	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