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Detailed information for vg0711201792:

Variant ID: vg0711201792 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11201792
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: 116. )

Flanking Sequence (100 bp) in Reference Genome:

ACTTGGACTGGGCCAACTCCCAATCGGCTTATTCTTTGCCGACAAGATCCAGTGTCGAGGAGAAATCACATCAACTCTGATGATGGATCGGCTGCTTAAC[C/T]
TCCCAGGACCCCCTCTGGGCAACATTGACAATATTGAGTTGGCAGGATTCAAGAGCAGAAACTTCGACAGATGGTGGGGTGAATGGAAGCTGCACATGTT

Reverse complement sequence

AACATGTGCAGCTTCCATTCACCCCACCATCTGTCGAAGTTTCTGCTCTTGAATCCTGCCAACTCAATATTGTCAATGTTGCCCAGAGGGGGTCCTGGGA[G/A]
GTTAAGCAGCCGATCCATCATCAGAGTTGATGTGATTTCTCCTCGACACTGGATCTTGTCGGCAAAGAATAAGCCGATTGGGAGTTGGCCCAGTCCAAGT

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	91.80%	3.20%	2.03%	2.96%	NA
All Indica	2759	94.10%	3.10%	2.75%	0.04%	NA
All Japonica	1512	86.60%	3.40%	0.79%	9.13%	NA
Aus	269	93.70%	3.70%	2.60%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	94.20%	2.20%	3.66%	0.00%	NA
Indica III	913	90.60%	5.70%	3.72%	0.00%	NA
Indica Intermediate	786	93.90%	2.90%	3.05%	0.13%	NA
Temperate Japonica	767	76.30%	6.50%	1.43%	15.78%	NA
Tropical Japonica	504	99.40%	0.20%	0.00%	0.40%	NA
Japonica Intermediate	241	92.90%	0.40%	0.41%	6.22%	NA
VI/Aromatic	96	93.80%	4.20%	1.04%	1.04%	NA
Intermediate	90	97.80%	2.20%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711201792	C -> DEL	N	N	silent_mutation	Average:20.031; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg0711201792	C -> T	LOC_Os07g18890.1	upstream_gene_variant ; 4619.0bp to feature; MODIFIER	silent_mutation	Average:20.031; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg0711201792	C -> T	LOC_Os07g18910.1	downstream_gene_variant ; 2121.0bp to feature; MODIFIER	silent_mutation	Average:20.031; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg0711201792	C -> T	LOC_Os07g18920.1	downstream_gene_variant ; 3650.0bp to feature; MODIFIER	silent_mutation	Average:20.031; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg0711201792	C -> T	LOC_Os07g18900.1	intron_variant ; MODIFIER	silent_mutation	Average:20.031; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711201792	1.00E-06	1.00E-06	mr1237	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
vg0711201792	1.59E-06	1.59E-06	mr1973	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