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Detailed information for vg0613080964:

Variant ID: vg0613080964 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13080964
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

CACTAAGAACCTTTGCGTAAACCTGATGGGCTTCTTAGGTGTATATGGGAAGTCCAAAGATACACTCGAAGCATGCAATGATCTCAAGCATATGGAACAA[T/C]
ACGAGGGCCTTCATCCAGAACCGAATGAGAAAGGAAGCCATTACTTGAGTCCGGCGAGCTACACCCTGAGCAAGGAAGAGAAGGATAGTATGTTTCAATG

Reverse complement sequence

CATTGAAACATACTATCCTTCTCTTCCTTGCTCAGGGTGTAGCTCGCCGGACTCAAGTAATGGCTTCCTTTCTCATTCGGTTCTGGATGAAGGCCCTCGT[A/G]
TTGTTCCATATGCTTGAGATCATTGCATGCTTCGAGTGTATCTTTGGACTTCCCATATACACCTAAGAAGCCCATCAGGTTTACGCAAAGGTTCTTAGTG

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	50.30%	37.50%	11.38%	0.83%	NA
All Indica	2759	75.20%	11.70%	12.43%	0.69%	NA
All Japonica	1512	9.20%	88.30%	1.32%	1.19%	NA
Aus	269	23.40%	25.30%	51.30%	0.00%	NA
Indica I	595	77.30%	8.20%	12.10%	2.35%	NA
Indica II	465	56.30%	27.70%	15.70%	0.22%	NA
Indica III	913	87.00%	1.80%	11.17%	0.11%	NA
Indica Intermediate	786	71.10%	16.30%	12.21%	0.38%	NA
Temperate Japonica	767	0.90%	95.30%	1.69%	2.09%	NA
Tropical Japonica	504	22.00%	77.20%	0.60%	0.20%	NA
Japonica Intermediate	241	8.70%	89.20%	1.66%	0.41%	NA
VI/Aromatic	96	67.70%	4.20%	28.12%	0.00%	NA
Intermediate	90	40.00%	46.70%	11.11%	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
vg0613080964	T -> C	LOC_Os06g22510.1	missense_variant ; p.Tyr341His; MODERATE	nonsynonymous_codon ; Y341R	Average:20.247; most accessible tissue: Zhenshan97 panicle, score: 28.447	possibly damaging	-1.618	TOLERATED	1.00
vg0613080964	T -> C	LOC_Os06g22510.1	missense_variant ; p.Tyr341His; MODERATE	nonsynonymous_codon ; Y341H	Average:20.247; most accessible tissue: Zhenshan97 panicle, score: 28.447	possibly damaging	-1.52	DELETERIOUS	0.03
vg0613080964	T -> DEL	LOC_Os06g22510.1	N	frameshift_variant	Average:20.247; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613080964	NA	1.30E-06	mr1886	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
vg0613080964	NA	2.01E-09	mr1979	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