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Detailed information for vg0110181846:

Variant ID: vg0110181846 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 10181846
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACAAGCGGCATCTCGTGCACCATCTCCTCCGGCTCCGCCATCTCCTCCTGCACCATCTCCTCCGGTTCCTCCGGCACGTCCTCCTGCACCATCTCCTCC[A/G]
GCTCCTCCGCCACCTCCTGCTGCACCATCTCCTCCGGCTCCTCCGCCTCCACCATGTCCGCCTGCACCTCCCAAGACAAGGTCTCGCCAAGCTCCGTCGC

Reverse complement sequence

GCGACGGAGCTTGGCGAGACCTTGTCTTGGGAGGTGCAGGCGGACATGGTGGAGGCGGAGGAGCCGGAGGAGATGGTGCAGCAGGAGGTGGCGGAGGAGC[T/C]
GGAGGAGATGGTGCAGGAGGACGTGCCGGAGGAACCGGAGGAGATGGTGCAGGAGGAGATGGCGGAGCCGGAGGAGATGGTGCACGAGATGCCGCTTGTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.40%	3.60%	5.88%	0.08%	NA
All Indica	2759	91.00%	3.40%	5.51%	0.14%	NA
All Japonica	1512	99.70%	0.00%	0.33%	0.00%	NA
Aus	269	29.40%	27.10%	43.49%	0.00%	NA
Indica I	595	98.20%	0.30%	1.18%	0.34%	NA
Indica II	465	86.20%	4.10%	9.46%	0.22%	NA
Indica III	913	88.90%	5.00%	5.91%	0.11%	NA
Indica Intermediate	786	90.70%	3.30%	5.98%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	95.80%	2.10%	2.08%	0.00%	NA
Intermediate	90	94.40%	3.30%	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
vg0110181846	A -> G	LOC_Os01g18190.1	synonymous_variant ; p.Pro334Pro; LOW	synonymous_codon	Average:36.1; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N
vg0110181846	A -> DEL	LOC_Os01g18190.1	N	frameshift_variant	Average:36.1; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0110181846	NA	2.46E-06	mr1291	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
vg0110181846	3.85E-06	NA	mr1265_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
vg0110181846	NA	6.27E-07	mr1369_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
vg0110181846	NA	1.21E-07	mr1453_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
vg0110181846	NA	6.10E-08	mr1683_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
vg0110181846	NA	2.67E-13	mr1838_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