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Detailed information for vg1111172103:

Variant ID: vg1111172103 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11172103
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTGATCCCGTTTAAAGCTATTGTTTCTATTCAACTATTGCATTTATTTTCGAATGTCATTGGGTGGAATTAACCTATTGTTTGTTATAGCCCTTTTGTT[C/T]
TTGATTACTTTATTCCTTAATACCTTGGGTTATTATAACTTGACTAGTTGGGCTATATATATTGGTTCAGCTAGATATTAGATATGATTGCTTAGCCATA

Reverse complement sequence

TATGGCTAAGCAATCATATCTAATATCTAGCTGAACCAATATATATAGCCCAACTAGTCAAGTTATAATAACCCAAGGTATTAAGGAATAAAGTAATCAA[G/A]
AACAAAAGGGCTATAACAAACAATAGGTTAATTCCACCCAATGACATTCGAAAATAAATGCAATAGTTGAATAGAAACAATAGCTTTAAACGGGATCAAC

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	83.50%	0.10%	7.66%	8.68%	NA
All Indica	2759	76.10%	0.30%	12.18%	11.49%	NA
All Japonica	1512	98.50%	0.00%	0.40%	1.12%	NA
Aus	269	71.00%	0.00%	5.20%	23.79%	NA
Indica I	595	53.90%	0.50%	20.34%	25.21%	NA
Indica II	465	80.90%	0.20%	11.18%	7.74%	NA
Indica III	913	87.80%	0.00%	7.34%	4.82%	NA
Indica Intermediate	786	76.30%	0.40%	12.21%	11.07%	NA
Temperate Japonica	767	99.20%	0.00%	0.65%	0.13%	NA
Tropical Japonica	504	97.20%	0.00%	0.00%	2.78%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	82.20%	0.00%	6.67%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111172103	C -> T	LOC_Os11g19430.1	upstream_gene_variant ; 1792.0bp to feature; MODIFIER	silent_mutation	Average:12.122; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1111172103	C -> T	LOC_Os11g19420.1	downstream_gene_variant ; 3992.0bp to feature; MODIFIER	silent_mutation	Average:12.122; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1111172103	C -> T	LOC_Os11g19420-LOC_Os11g19430	intergenic_region ; MODIFIER	silent_mutation	Average:12.122; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1111172103	C -> DEL	N	N	silent_mutation	Average:12.122; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111172103	7.24E-07	3.25E-06	mr1128	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
vg1111172103	6.63E-06	6.63E-06	mr1341_2	Ind_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