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Detailed information for vg1122450251:

Variant ID: vg1122450251 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22450251
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTGTCATCCTTTCTTTTTCTAATAAACTAGAAAAAATACCCGTGCATTACAGCGGGTGAAGACTATTTTAGTTTTATTATTATTGTTATACGATTTAG[T/C]
TAGGGTGAAAATCATTGTGGGAATTTACTTGGATATTTTTTTTAGAAAATCATGAGTTGTAATTAGGAGTTCGACTCTTATCTCAAGTTAGCATCTCAAG

Reverse complement sequence

CTTGAGATGCTAACTTGAGATAAGAGTCGAACTCCTAATTACAACTCATGATTTTCTAAAAAAAATATCCAAGTAAATTCCCACAATGATTTTCACCCTA[A/G]
CTAAATCGTATAACAATAATAATAAAACTAAAATAGTCTTCACCCGCTGTAATGCACGGGTATTTTTTCTAGTTTATTAGAAAAAGAAAGGATGACAAAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.40%	17.60%	0.21%	6.77%	NA
All Indica	2759	99.10%	0.60%	0.00%	0.25%	NA
All Japonica	1512	25.80%	53.20%	0.53%	20.44%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.90%	0.60%	0.00%	0.43%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.00%	0.00%	0.64%	NA
Temperate Japonica	767	21.50%	67.70%	0.13%	10.69%	NA
Tropical Japonica	504	22.60%	46.40%	0.79%	30.16%	NA
Japonica Intermediate	241	46.10%	21.60%	1.24%	31.12%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	10.00%	2.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122450251	T -> DEL	N	N	silent_mutation	Average:43.602; most accessible tissue: Zhenshan97 root, score: 84.212	N	N	N	N
vg1122450251	T -> C	LOC_Os11g37880.1	upstream_gene_variant ; 1385.0bp to feature; MODIFIER	silent_mutation	Average:43.602; most accessible tissue: Zhenshan97 root, score: 84.212	N	N	N	N
vg1122450251	T -> C	LOC_Os11g37870.1	downstream_gene_variant ; 4858.0bp to feature; MODIFIER	silent_mutation	Average:43.602; most accessible tissue: Zhenshan97 root, score: 84.212	N	N	N	N
vg1122450251	T -> C	LOC_Os11g37870-LOC_Os11g37880	intergenic_region ; MODIFIER	silent_mutation	Average:43.602; most accessible tissue: Zhenshan97 root, score: 84.212	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122450251	4.12E-06	4.12E-06	mr1333	Jap_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
vg1122450251	NA	6.48E-06	mr1686	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
vg1122450251	NA	5.62E-06	mr1928	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