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Detailed information for vg0900275938:

Variant ID: vg0900275938 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 275938
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

ACTGGGCAACGGCGCATGTGTGTCGATTATACCGACCTCAACAAGCCTTGCCCTAAAGATCCTTTCGGGTTGCCTCGCATTGACCAGGTAGTCGACTCGA[C/T]
CGCCGGCTGCGAGCTACTCAGTTTCCTGGATTGCTACTTGAGATATCATCAGATCCGACTGAAGGAATCCGACTGCTTGAAGACCTCATTCATTACGCCC

Reverse complement sequence

GGGCGTAATGAATGAGGTCTTCAAGCAGTCGGATTCCTTCAGTCGGATCTGATGATATCTCAAGTAGCAATCCAGGAAACTGAGTAGCTCGCAGCCGGCG[G/A]
TCGAGTCGACTACCTGGTCAATGCGAGGCAACCCGAAAGGATCTTTAGGGCAAGGCTTGTTGAGGTCGGTATAATCGACACACATGCGCCGTTGCCCAGT

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	42.60%	39.50%	12.25%	5.65%	NA
All Indica	2759	67.00%	13.20%	18.41%	1.34%	NA
All Japonica	1512	0.50%	84.30%	0.86%	14.42%	NA
Aus	269	50.60%	27.50%	18.59%	3.35%	NA
Indica I	595	64.00%	16.00%	17.98%	2.02%	NA
Indica II	465	68.40%	12.70%	18.06%	0.86%	NA
Indica III	913	74.40%	11.00%	14.13%	0.55%	NA
Indica Intermediate	786	59.90%	14.10%	23.92%	2.04%	NA
Temperate Japonica	767	0.80%	71.20%	0.78%	27.25%	NA
Tropical Japonica	504	0.00%	99.60%	0.40%	0.00%	NA
Japonica Intermediate	241	0.40%	93.80%	2.07%	3.73%	NA
VI/Aromatic	96	0.00%	97.90%	1.04%	1.04%	NA
Intermediate	90	22.20%	67.80%	7.78%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900275938	C -> DEL	LOC_Os09g01340.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900275938	C -> T	LOC_Os09g01340.1	missense_variant ; p.Thr1059Ile; MODERATE	nonsynonymous_codon ; T1059I	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	benign	0.856	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900275938	NA	7.62E-06	mr1625	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
vg0900275938	NA	9.24E-08	mr1782	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