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Detailed information for vg0210408970:

Variant ID: vg0210408970 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10408970
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CATTATTTGTGTGGATGGTACCGTGTACAGGTATCTTAAGGGATCGAAGAAGCTAGTGTACATGCGGCACCGGCGTTTCTTAAGAAAGAATCACTCGTAC[C/T]
ACTCCCAAGCAGAATATTTCGACGGTACTGTTGAGAAAGGTGTAGCACCAGAACCATGGAAGGGTGATAAAATGTTCAGAATGACAAAAACCTGAAGGTT

Reverse complement sequence

AACCTTCAGGTTTTTGTCATTCTGAACATTTTATCACCCTTCCATGGTTCTGGTGCTACACCTTTCTCAACAGTACCGTCGAAATATTCTGCTTGGGAGT[G/A]
GTACGAGTGATTCTTTCTTAAGAAACGCCGGTGCCGCATGTACACTAGCTTCTTCGATCCCTTAAGATACCTGTACACGGTACCATCCACACAAATAATG

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	74.80%	7.20%	6.09%	12.00%	NA
All Indica	2759	62.40%	8.70%	8.77%	20.19%	NA
All Japonica	1512	99.20%	0.40%	0.20%	0.20%	NA
Aus	269	55.00%	30.90%	14.13%	0.00%	NA
Indica I	595	85.40%	6.90%	1.68%	6.05%	NA
Indica II	465	48.40%	10.80%	7.31%	33.55%	NA
Indica III	913	54.30%	5.70%	15.22%	24.75%	NA
Indica Intermediate	786	62.60%	12.20%	7.51%	17.68%	NA
Temperate Japonica	767	99.10%	0.50%	0.13%	0.26%	NA
Tropical Japonica	504	99.20%	0.20%	0.40%	0.20%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	10.00%	5.56%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210408970	C -> T	LOC_Os02g17960.1	missense_variant ; p.His466Tyr; MODERATE	nonsynonymous_codon ; H466C	Average:44.801; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	unknown	unknown	DELETERIOUS	0.03
vg0210408970	C -> DEL	LOC_Os02g17960.1	N	frameshift_variant	Average:44.801; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210408970	3.43E-06	3.43E-06	mr1360	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