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Detailed information for vg0711419116:

Variant ID: vg0711419116 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11419116
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGGAGTGACGAAGGCGGTGGAGGTAAGGATGGCGGCGACGGTGAGAGAAGAGAGAACGAGCGAGAGAGAGGGGAAAGAGAGAGACGGCGCTCTCTCTC[C/T]
CGCTCCGAACACGTGCGGCGCACGCGCAGGAGAGAGCTGGGCCGAGAGGAGGGGATGGGCCGGGAGAGAGGAACAGCCCATCGACAAGGGAGGCAAAATA

Reverse complement sequence

TATTTTGCCTCCCTTGTCGATGGGCTGTTCCTCTCTCCCGGCCCATCCCCTCCTCTCGGCCCAGCTCTCTCCTGCGCGTGCGCCGCACGTGTTCGGAGCG[G/A]
GAGAGAGAGCGCCGTCTCTCTCTTTCCCCTCTCTCTCGCTCGTTCTCTCTTCTCTCACCGTCGCCGCCATCCTTACCTCCACCGCCTTCGTCACTCCGGC

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	46.70%	0.60%	0.95%	51.78%	NA
All Indica	2759	21.50%	1.00%	1.52%	75.93%	NA
All Japonica	1512	94.10%	0.00%	0.00%	5.89%	NA
Aus	269	23.40%	0.40%	0.37%	75.84%	NA
Indica I	595	36.30%	0.00%	1.51%	62.18%	NA
Indica II	465	16.60%	1.30%	0.86%	81.29%	NA
Indica III	913	6.80%	1.40%	1.75%	90.03%	NA
Indica Intermediate	786	30.40%	1.10%	1.65%	66.79%	NA
Temperate Japonica	767	98.40%	0.00%	0.00%	1.56%	NA
Tropical Japonica	504	86.90%	0.00%	0.00%	13.10%	NA
Japonica Intermediate	241	95.40%	0.00%	0.00%	4.56%	NA
VI/Aromatic	96	80.20%	0.00%	0.00%	19.79%	NA
Intermediate	90	53.30%	0.00%	2.22%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711419116	C -> DEL	N	N	silent_mutation	Average:18.627; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0711419116	C -> T	LOC_Os07g19300.1	upstream_gene_variant ; 1440.0bp to feature; MODIFIER	silent_mutation	Average:18.627; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0711419116	C -> T	LOC_Os07g19290.1	intron_variant ; MODIFIER	silent_mutation	Average:18.627; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711419116	3.24E-06	3.24E-06	mr1972_2	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
vg0711419116	3.45E-06	2.33E-06	mr1972_2	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