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Detailed information for vg0114021291:

Variant ID: vg0114021291 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14021291
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

AATGTACATATATTACATTTGTTGCCAATATATATATATTACAATATGTTTTTATATTATCACTTCAAATACGCCATCTAGTTAATACATTATGTTATAG[C/T]
ACTGTTCCACTCCCGAAGATCCTTGAATTCGTCACTTGTGGCTAGGGCACCCTCTGGGTTGAAGAAATCTCCTTTCACATGACAGCAATCATAGTGGATG

Reverse complement sequence

CATCCACTATGATTGCTGTCATGTGAAAGGAGATTTCTTCAACCCAGAGGGTGCCCTAGCCACAAGTGACGAATTCAAGGATCTTCGGGAGTGGAACAGT[G/A]
CTATAACATAATGTATTAACTAGATGGCGTATTTGAAGTGATAATATAAAAACATATTGTAATATATATATATTGGCAACAAATGTAATATATGTACATT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.20%	10.30%	14.62%	14.88%	NA
All Indica	2759	42.00%	17.30%	21.09%	19.64%	NA
All Japonica	1512	99.70%	0.10%	0.00%	0.13%	NA
Aus	269	8.90%	0.70%	36.80%	53.53%	NA
Indica I	595	20.00%	34.10%	28.07%	17.82%	NA
Indica II	465	54.80%	29.90%	11.18%	4.09%	NA
Indica III	913	49.00%	0.50%	23.00%	27.49%	NA
Indica Intermediate	786	43.00%	16.40%	19.47%	21.12%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	73.30%	5.60%	11.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114021291	C -> T	LOC_Os01g24890.1	missense_variant ; p.Ala814Thr; MODERATE	nonsynonymous_codon ; A814T	Average:37.769; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	unknown	unknown	TOLERATED	0.12
vg0114021291	C -> DEL	LOC_Os01g24890.1	N	frameshift_variant	Average:37.769; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114021291	8.36E-06	8.32E-06	mr1267	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