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Detailed information for vg1114473442:

Variant ID: vg1114473442 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14473442
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGCAGGTTCGTGTGGGTTCACGGCCTTGATTAATAATATTGTATAGCTTTGGAATCGTGTTTACAAAATAGCTTTGAGCAACTAAGAGTCTTTTAATGC[T/C]
GTTTACTGCAAACCCTAACCCTTTATATTATAACCCCCTTGTACTCCCTTGCATTTATCCTGCACTTGTGGGTGTGTCTTGTTGAGTACGGTGGTTGTAC

Reverse complement sequence

GTACAACCACCGTACTCAACAAGACACACCCACAAGTGCAGGATAAATGCAAGGGAGTACAAGGGGGTTATAATATAAAGGGTTAGGGTTTGCAGTAAAC[A/G]
GCATTAAAAGACTCTTAGTTGCTCAAAGCTATTTTGTAAACACGATTCCAAAGCTATACAATATTATTAATCAAGGCCGTGAACCCACACGAACCTGCCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.90%	18.90%	21.82%	5.40%	NA
All Indica	2759	25.40%	31.10%	35.01%	8.52%	NA
All Japonica	1512	97.40%	0.60%	1.65%	0.40%	NA
Aus	269	87.00%	0.70%	8.55%	3.72%	NA
Indica I	595	25.00%	22.50%	45.71%	6.72%	NA
Indica II	465	12.90%	32.90%	40.22%	13.98%	NA
Indica III	913	30.70%	35.80%	26.51%	7.01%	NA
Indica Intermediate	786	27.00%	30.90%	33.72%	8.40%	NA
Temperate Japonica	767	96.60%	0.80%	2.35%	0.26%	NA
Tropical Japonica	504	98.00%	0.40%	0.99%	0.60%	NA
Japonica Intermediate	241	98.30%	0.40%	0.83%	0.41%	NA
VI/Aromatic	96	86.50%	11.50%	2.08%	0.00%	NA
Intermediate	90	61.10%	17.80%	16.67%	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
vg1114473442	T -> DEL	N	N	silent_mutation	Average:10.87; most accessible tissue: Callus, score: 16.428	N	N	N	N
vg1114473442	T -> C	LOC_Os11g25380.1	downstream_gene_variant ; 4527.0bp to feature; MODIFIER	silent_mutation	Average:10.87; most accessible tissue: Callus, score: 16.428	N	N	N	N
vg1114473442	T -> C	LOC_Os11g25390.1	intron_variant ; MODIFIER	silent_mutation	Average:10.87; most accessible tissue: Callus, score: 16.428	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114473442	1.57E-06	NA	mr1089	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
vg1114473442	NA	6.09E-07	mr1089	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
vg1114473442	1.76E-09	NA	mr1109	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
vg1114473442	1.54E-06	8.17E-12	mr1109	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
vg1114473442	5.28E-08	1.35E-36	mr1129	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
vg1114473442	NA	3.08E-11	mr1129	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
vg1114473442	7.71E-07	NA	mr1235	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
vg1114473442	NA	1.01E-07	mr1235	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
vg1114473442	6.30E-08	NA	mr1243	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
vg1114473442	2.52E-06	1.62E-07	mr1243	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
vg1114473442	8.58E-09	1.51E-31	mr1251	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
vg1114473442	1.97E-06	4.26E-11	mr1251	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
vg1114473442	6.31E-07	3.16E-22	mr1253	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
vg1114473442	3.55E-06	2.13E-08	mr1253	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
vg1114473442	2.55E-08	4.27E-29	mr1255	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
vg1114473442	NA	9.23E-10	mr1255	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
vg1114473442	4.12E-10	1.87E-38	mr1257	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
vg1114473442	3.57E-07	2.32E-12	mr1257	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
vg1114473442	NA	9.26E-07	mr1377	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
vg1114473442	1.23E-08	NA	mr1423	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
vg1114473442	3.76E-07	4.91E-10	mr1423	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
vg1114473442	2.05E-07	NA	mr1435	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
vg1114473442	NA	9.20E-10	mr1435	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
vg1114473442	1.02E-08	NA	mr1599	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
vg1114473442	9.99E-07	1.90E-09	mr1599	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
vg1114473442	NA	2.62E-07	mr1089_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
vg1114473442	1.91E-06	NA	mr1109_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
vg1114473442	NA	4.19E-11	mr1109_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
vg1114473442	1.27E-07	2.41E-38	mr1129_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
vg1114473442	NA	5.63E-14	mr1129_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
vg1114473442	NA	1.06E-06	mr1236_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
vg1114473442	NA	1.66E-06	mr1236_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
vg1114473442	NA	2.26E-08	mr1251_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
vg1114473442	NA	3.61E-21	mr1253_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
vg1114473442	1.20E-08	2.48E-32	mr1255_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
vg1114473442	3.16E-06	5.95E-13	mr1255_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
vg1114473442	2.94E-06	2.28E-37	mr1257_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
vg1114473442	NA	2.16E-11	mr1257_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
vg1114473442	NA	2.10E-06	mr1423_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
vg1114473442	NA	2.09E-08	mr1435_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