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Detailed information for vg1118414920:

Variant ID: vg1118414920 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18414920
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACACATGATGATCTCACAATAGTGAACCAGGTGCATTTTAGATTGTTAGACTTCCTGGTGAAAACCTGAAAGCCTCAGGCTGTCAGTGCTAGTCTCATTT[C/G]
AACAAAATGCAAATTAGTGGCAAATATGCAAAAAAGAAGCTTCAGTTCCTTCACTGACAAATACTCAAAAGTCCTTAGTACTCTTTTCCGGTGAAGGGAA

Reverse complement sequence

TTCCCTTCACCGGAAAAGAGTACTAAGGACTTTTGAGTATTTGTCAGTGAAGGAACTGAAGCTTCTTTTTTGCATATTTGCCACTAATTTGCATTTTGTT[G/C]
AAATGAGACTAGCACTGACAGCCTGAGGCTTTCAGGTTTTCACCAGGAAGTCTAACAATCTAAAATGCACCTGGTTCACTATTGTGAGATCATCATGTGT

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	61.00%	38.90%	0.08%	0.00%	NA
All Indica	2759	89.20%	10.80%	0.07%	0.00%	NA
All Japonica	1512	5.00%	95.00%	0.00%	0.00%	NA
Aus	269	84.40%	15.60%	0.00%	0.00%	NA
Indica I	595	77.50%	22.50%	0.00%	0.00%	NA
Indica II	465	93.30%	6.70%	0.00%	0.00%	NA
Indica III	913	96.20%	3.70%	0.11%	0.00%	NA
Indica Intermediate	786	87.40%	12.50%	0.13%	0.00%	NA
Temperate Japonica	767	5.50%	94.50%	0.00%	0.00%	NA
Tropical Japonica	504	2.80%	97.20%	0.00%	0.00%	NA
Japonica Intermediate	241	8.30%	91.70%	0.00%	0.00%	NA
VI/Aromatic	96	70.80%	29.20%	0.00%	0.00%	NA
Intermediate	90	57.80%	40.00%	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
vg1118414920	C -> G	LOC_Os11g31510.1	upstream_gene_variant ; 2125.0bp to feature; MODIFIER	silent_mutation	Average:34.559; most accessible tissue: Zhenshan97 young leaf, score: 58.398	N	N	N	N
vg1118414920	C -> G	LOC_Os11g31520.1	upstream_gene_variant ; 4103.0bp to feature; MODIFIER	silent_mutation	Average:34.559; most accessible tissue: Zhenshan97 young leaf, score: 58.398	N	N	N	N
vg1118414920	C -> G	LOC_Os11g31500.1	intron_variant ; MODIFIER	silent_mutation	Average:34.559; most accessible tissue: Zhenshan97 young leaf, score: 58.398	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118414920	NA	9.45E-06	mr1002	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
vg1118414920	NA	5.86E-11	mr1322	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
vg1118414920	NA	6.38E-12	mr1325	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
vg1118414920	NA	8.61E-14	mr1326	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
vg1118414920	NA	3.68E-08	mr1527	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
vg1118414920	NA	3.02E-09	mr1532	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
vg1118414920	NA	3.11E-08	mr1659	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
vg1118414920	NA	4.04E-07	mr1690	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
vg1118414920	NA	1.27E-06	mr1002_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