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Detailed information for vg1121744807:

Variant ID: vg1121744807 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21744807
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.06, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

GGATGGTTGGCTCTGATACCTATTATTACGATCTCTCTATCCTTCCAGCACTTTGGGAAATTTGGGGAAAGGGATGAACTGGAGAGAAGCAGAGGAAGAA[C/T]
AGAGAAAACTTGGGAGAGAGAGAGATAGCAGTAGTTGGGAGGGATTTGATTTCTCAGTTTTCTTATTCGATACCCTTCTCCAAGTCGTCATATGTGCTTA

Reverse complement sequence

TAAGCACATATGACGACTTGGAGAAGGGTATCGAATAAGAAAACTGAGAAATCAAATCCCTCCCAACTACTGCTATCTCTCTCTCTCCCAAGTTTTCTCT[G/A]
TTCTTCCTCTGCTTCTCTCCAGTTCATCCCTTTCCCCAAATTTCCCAAAGTGCTGGAAGGATAGAGAGATCGTAATAATAGGTATCAGAGCCAACCATCC

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	45.80%	19.40%	3.96%	30.89%	NA
All Indica	2759	22.40%	29.10%	4.35%	44.07%	NA
All Japonica	1512	82.10%	5.40%	2.38%	10.12%	NA
Aus	269	85.50%	1.50%	4.83%	8.18%	NA
Indica I	595	39.20%	30.40%	4.03%	26.39%	NA
Indica II	465	3.70%	37.40%	3.87%	55.05%	NA
Indica III	913	24.80%	19.70%	4.82%	50.71%	NA
Indica Intermediate	786	18.20%	34.20%	4.33%	43.26%	NA
Temperate Japonica	767	90.40%	4.60%	0.52%	4.56%	NA
Tropical Japonica	504	76.00%	5.80%	2.98%	15.28%	NA
Japonica Intermediate	241	68.50%	7.50%	7.05%	17.01%	NA
VI/Aromatic	96	30.20%	6.20%	9.38%	54.17%	NA
Intermediate	90	48.90%	22.20%	10.00%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121744807	C -> T	LOC_Os11g36850.1	upstream_gene_variant ; 3708.0bp to feature; MODIFIER	silent_mutation	Average:63.066; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N
vg1121744807	C -> T	LOC_Os11g36860.1	upstream_gene_variant ; 265.0bp to feature; MODIFIER	silent_mutation	Average:63.066; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N
vg1121744807	C -> T	LOC_Os11g36870.1	upstream_gene_variant ; 1243.0bp to feature; MODIFIER	silent_mutation	Average:63.066; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N
vg1121744807	C -> T	LOC_Os11g36860-LOC_Os11g36870	intergenic_region ; MODIFIER	silent_mutation	Average:63.066; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N
vg1121744807	C -> DEL	N	N	silent_mutation	Average:63.066; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121744807	7.62E-07	3.20E-09	mr1698	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
vg1121744807	3.25E-06	1.12E-08	mr1698_2	Jap_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