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Detailed information for vg0126542310:

Variant ID: vg0126542310 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 26542310
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGACTCGGCTGGGACAGGCGTCGCCGGCCCCGCAGCAGCCGAATCCATCGCCCCACATGCACGATGGCCGGATCCGTGCCACCGCCGCCGAGATTCCTAG[T/G]
GGTTTGATTTTTTTTATTTTTATTTTTATGCGCGGACGACATAAGCACCCGCACGTGAAAAATCGGATTTTTGCAGACCATTTAGGGCAGAAGGGTTAGG

Reverse complement sequence

CCTAACCCTTCTGCCCTAAATGGTCTGCAAAAATCCGATTTTTCACGTGCGGGTGCTTATGTCGTCCGCGCATAAAAATAAAAATAAAAAAAATCAAACC[A/C]
CTAGGAATCTCGGCGGCGGTGGCACGGATCCGGCCATCGTGCATGTGGGGCGATGGATTCGGCTGCTGCGGGGCCGGCGACGCCTGTCCCAGCCGAGTCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.50%	3.70%	0.02%	0.76%	NA
All Indica	2759	98.90%	1.00%	0.00%	0.07%	NA
All Japonica	1512	97.80%	0.00%	0.00%	2.25%	NA
Aus	269	48.00%	51.70%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.50%	1.40%	0.00%	0.11%	NA
Indica Intermediate	786	98.00%	1.90%	0.00%	0.13%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	93.80%	0.00%	0.00%	6.15%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0126542310	T -> G	LOC_Os01g46620.1	upstream_gene_variant ; 1537.0bp to feature; MODIFIER	silent_mutation	Average:73.264; most accessible tissue: Minghui63 young leaf, score: 83.166	N	N	N	N
vg0126542310	T -> G	LOC_Os01g46626.1	downstream_gene_variant ; 3471.0bp to feature; MODIFIER	silent_mutation	Average:73.264; most accessible tissue: Minghui63 young leaf, score: 83.166	N	N	N	N
vg0126542310	T -> G	LOC_Os01g46620-LOC_Os01g46626	intergenic_region ; MODIFIER	silent_mutation	Average:73.264; most accessible tissue: Minghui63 young leaf, score: 83.166	N	N	N	N
vg0126542310	T -> DEL	N	N	silent_mutation	Average:73.264; most accessible tissue: Minghui63 young leaf, score: 83.166	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0126542310	NA	4.45E-06	mr1004	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
vg0126542310	NA	2.39E-06	mr1006	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
vg0126542310	NA	1.93E-07	mr1028	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
vg0126542310	NA	2.90E-06	mr1052	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
vg0126542310	NA	4.50E-08	mr1126	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
vg0126542310	NA	1.25E-07	mr1286	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
vg0126542310	NA	4.83E-07	mr1321	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
vg0126542310	NA	1.32E-10	mr1369	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
vg0126542310	NA	3.90E-09	mr1453	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
vg0126542310	NA	3.92E-07	mr1651	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
vg0126542310	NA	4.00E-08	mr1652	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
vg0126542310	NA	5.08E-07	mr1665	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