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Detailed information for vg1124929928:

Variant ID: vg1124929928 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24929928
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGTGTGTTATGGCAGGGAGCACTGTATGTGCATTCTGGAGGGGCTTGTGTTACAAGGTAAAAAAAAAAAAACATCACCACTCTATATATGTTTTGCCAT[G/C]
AATTTTATCGATTCATTGCAATTTTGATTGATAGATATATCTTTTGCTTAAATTGTCAACAAATAGTTAATAAAAAGGGTTTTTTGTCTTTATAGCTGAT

Reverse complement sequence

ATCAGCTATAAAGACAAAAAACCCTTTTTATTAACTATTTGTTGACAATTTAAGCAAAAGATATATCTATCAATCAAAATTGCAATGAATCGATAAAATT[C/G]
ATGGCAAAACATATATAGAGTGGTGATGTTTTTTTTTTTTTACCTTGTAACACAAGCCCCTCCAGAATGCACATACAGTGCTCCCTGCCATAACACACTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.80%	6.20%	0.02%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	83.30%	16.60%	0.07%	0.00%	NA
Aus	269	88.80%	11.20%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	91.90%	8.10%	0.00%	0.00%	NA
Tropical Japonica	504	76.40%	23.40%	0.20%	0.00%	NA
Japonica Intermediate	241	70.50%	29.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg1124929928	G -> C	LOC_Os11g41560.1	upstream_gene_variant ; 2613.0bp to feature; MODIFIER	silent_mutation	Average:70.975; most accessible tissue: Minghui63 flag leaf, score: 85.327	N	N	N	N
vg1124929928	G -> C	LOC_Os11g41550.1	intron_variant ; MODIFIER	silent_mutation	Average:70.975; most accessible tissue: Minghui63 flag leaf, score: 85.327	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124929928	1.21E-08	NA	mr1238	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
vg1124929928	NA	2.72E-07	mr1238	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
vg1124929928	2.73E-10	NA	mr1238_2	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
vg1124929928	5.22E-07	2.55E-08	mr1238_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
vg1124929928	NA	5.74E-06	mr1388_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
vg1124929928	1.81E-08	NA	mr1484_2	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
vg1124929928	1.52E-06	1.52E-06	mr1484_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
vg1124929928	3.28E-09	NA	mr1841_2	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
vg1124929928	3.37E-06	4.61E-08	mr1841_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
vg1124929928	2.80E-06	NA	mr1900_2	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
vg1124929928	NA	2.41E-06	mr1900_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
vg1124929928	3.44E-09	NA	mr1945_2	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
vg1124929928	9.47E-08	9.47E-08	mr1945_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