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Detailed information for vg1110149954:

Variant ID: vg1110149954 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10149954
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCTTTCTTCCTTGTCATCTTATGAACTGAGCTAACAAATCCAACATTCACGCTTTTCGTATCCGTAGACTAAATTCCTAATAATTTGAGAAAATTCACC[G/A]
TTGTCTTGAATCACCCGAAGAAATTCCTCTTCAGTGACGCAGATTTTCATATATTCCCATCATGTCGATCTGCATATCTTGGATATATCCTGTACTGCTA

Reverse complement sequence

TAGCAGTACAGGATATATCCAAGATATGCAGATCGACATGATGGGAATATATGAAAATCTGCGTCACTGAAGAGGAATTTCTTCGGGTGATTCAAGACAA[C/T]
GGTGAATTTTCTCAAATTATTAGGAATTTAGTCTACGGATACGAAAAGCGTGAATGTTGGATTTGTTAGCTCAGTTCATAAGATGACAAGGAAGAAAGGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.90%	2.60%	3.79%	20.74%	NA
All Indica	2759	58.60%	4.30%	5.40%	31.71%	NA
All Japonica	1512	96.50%	0.00%	0.66%	2.84%	NA
Aus	269	94.40%	0.40%	4.09%	1.12%	NA
Indica I	595	41.20%	0.00%	10.08%	48.74%	NA
Indica II	465	73.30%	13.30%	6.02%	7.31%	NA
Indica III	913	51.00%	3.20%	3.07%	42.72%	NA
Indica Intermediate	786	71.80%	3.60%	4.20%	20.48%	NA
Temperate Japonica	767	99.10%	0.00%	0.78%	0.13%	NA
Tropical Japonica	504	92.90%	0.00%	0.60%	6.55%	NA
Japonica Intermediate	241	95.90%	0.00%	0.41%	3.73%	NA
VI/Aromatic	96	43.80%	1.00%	5.21%	50.00%	NA
Intermediate	90	82.20%	1.10%	4.44%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110149954	G -> A	LOC_Os11g18044-LOC_Os11g18070	intergenic_region ; MODIFIER	silent_mutation	Average:46.078; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg1110149954	G -> DEL	N	N	silent_mutation	Average:46.078; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110149954	NA	2.95E-06	mr1049	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
vg1110149954	NA	1.12E-06	mr1053	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
vg1110149954	4.09E-06	4.09E-06	mr1058	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
vg1110149954	NA	9.57E-06	mr1122	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
vg1110149954	NA	3.53E-06	mr1720	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