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Detailed information for vg1103053802:

Variant ID: vg1103053802 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 3053802
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAGAAAGCATGGCGTGCAGCGCCCCGACGCAAGCATTGGCGTTGGAGAGGACGCGGCGAAGCTGGACGCCGACTACGGTGTCTCGTGCGCCGCGCCGGC[C/T]
GGTGGACCTGGAGGATGCCTGCAACCACTGGCTCGGCCTCGACACGGACTCACGGAGAAGCCAAGCGTCACCATAAGCAACTAGGAGAAACGGGATCTCG

Reverse complement sequence

CGAGATCCCGTTTCTCCTAGTTGCTTATGGTGACGCTTGGCTTCTCCGTGAGTCCGTGTCGAGGCCGAGCCAGTGGTTGCAGGCATCCTCCAGGTCCACC[G/A]
GCCGGCGCGGCGCACGAGACACCGTAGTCGGCGTCCAGCTTCGCCGCGTCCTCTCCAACGCCAATGCTTGCGTCGGGGCGCTGCACGCCATGCTTTCTTG

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	88.60%	8.80%	1.29%	1.29%	NA
All Indica	2759	90.00%	8.70%	0.76%	0.54%	NA
All Japonica	1512	84.90%	10.30%	2.31%	2.51%	NA
Aus	269	97.00%	0.00%	1.12%	1.86%	NA
Indica I	595	86.40%	11.80%	1.85%	0.00%	NA
Indica II	465	93.10%	6.70%	0.22%	0.00%	NA
Indica III	913	88.80%	9.70%	0.00%	1.42%	NA
Indica Intermediate	786	92.20%	6.40%	1.15%	0.25%	NA
Temperate Japonica	767	97.10%	0.90%	1.96%	0.00%	NA
Tropical Japonica	504	65.50%	25.00%	2.18%	7.34%	NA
Japonica Intermediate	241	86.30%	9.50%	3.73%	0.41%	NA
VI/Aromatic	96	87.50%	9.40%	0.00%	3.12%	NA
Intermediate	90	84.40%	13.30%	2.22%	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
vg1103053802	C -> T	LOC_Os11g06360.1	downstream_gene_variant ; 1302.0bp to feature; MODIFIER	silent_mutation	Average:76.165; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg1103053802	C -> T	LOC_Os11g06350-LOC_Os11g06360	intergenic_region ; MODIFIER	silent_mutation	Average:76.165; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg1103053802	C -> DEL	N	N	silent_mutation	Average:76.165; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1103053802	NA	1.32E-06	mr1519_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
vg1103053802	7.14E-06	2.60E-06	mr1527_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