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Detailed information for vg0224408464:

Variant ID: vg0224408464 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24408464
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCCAAAATCTCCCATCCAGTCAGGTCATCCCCAATCCCGTACATGGCATCCGGCATGGCGGCATCCCCAACCCTAGCGAGCACAGACAATGCGAGCTGA[C/T]
GGCACAGCGGCACGCGGCATGCAAGGCACCGGTGTGCCATGGGCCTGTGGTGAGGGCTGTTGTGCAAGGCAGGGCAGGCCACGCAGCGGTACTGGCAGCG

Reverse complement sequence

CGCTGCCAGTACCGCTGCGTGGCCTGCCCTGCCTTGCACAACAGCCCTCACCACAGGCCCATGGCACACCGGTGCCTTGCATGCCGCGTGCCGCTGTGCC[G/A]
TCAGCTCGCATTGTCTGTGCTCGCTAGGGTTGGGGATGCCGCCATGCCGGATGCCATGTACGGGATTGGGGATGACCTGACTGGATGGGAGATTTTGGAT

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	82.70%	3.40%	0.53%	13.33%	NA
All Indica	2759	87.60%	2.10%	0.51%	9.79%	NA
All Japonica	1512	72.80%	5.60%	0.66%	21.03%	NA
Aus	269	87.70%	3.00%	0.37%	8.92%	NA
Indica I	595	75.50%	2.70%	1.18%	20.67%	NA
Indica II	465	97.60%	0.00%	0.00%	2.37%	NA
Indica III	913	88.10%	1.20%	0.22%	10.51%	NA
Indica Intermediate	786	90.50%	3.80%	0.64%	5.09%	NA
Temperate Japonica	767	71.30%	3.80%	1.04%	23.86%	NA
Tropical Japonica	504	80.60%	8.50%	0.20%	10.71%	NA
Japonica Intermediate	241	61.00%	5.00%	0.41%	33.61%	NA
VI/Aromatic	96	84.40%	11.50%	0.00%	4.17%	NA
Intermediate	90	82.20%	2.20%	0.00%	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
vg0224408464	C -> T	LOC_Os02g40320.1	missense_variant ; p.Arg14His; MODERATE	nonsynonymous_codon ; R14H	Average:75.602; most accessible tissue: Minghui63 young leaf, score: 82.087	unknown	unknown	DELETERIOUS	0.00
vg0224408464	C -> DEL	LOC_Os02g40320.1	N	frameshift_variant	Average:75.602; most accessible tissue: Minghui63 young leaf, score: 82.087	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224408464	1.32E-09	1.32E-09	mr1470	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