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Detailed information for vg0123406476:

Variant ID: vg0123406476 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23406476
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCTTTGACACCTCCGAAGATCATCTCCCTATACAGAGTTTTGGTAGTAAATTCTCCTGTTTTTGTCAATTTCCATATCATTGTGTCTTTGTTAGAAGT[T/C]
AGCTGTATGTCTCTTAGTTTCTCATGCAAATCATTCCACTCCCCTACTTCTCTGTTTCCAATTGTTCTTCTTATACCAATCTCCCATTCCCCCCAGTGTT

Reverse complement sequence

AACACTGGGGGGAATGGGAGATTGGTATAAGAAGAACAATTGGAAACAGAGAAGTAGGGGAGTGGAATGATTTGCATGAGAAACTAAGAGACATACAGCT[A/G]
ACTTCTAACAAAGACACAATGATATGGAAATTGACAAAAACAGGAGAATTTACTACCAAAACTCTGTATAGGGAGATGATCTTCGGAGGTGTCAAAGATA

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	75.10%	24.90%	0.00%	0.00%	NA
All Indica	2759	85.00%	15.00%	0.00%	0.00%	NA
All Japonica	1512	52.40%	47.60%	0.00%	0.00%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	91.80%	8.20%	0.00%	0.00%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	71.90%	28.10%	0.00%	0.00%	NA
Indica Intermediate	786	88.70%	11.30%	0.00%	0.00%	NA
Temperate Japonica	767	37.20%	62.80%	0.00%	0.00%	NA
Tropical Japonica	504	81.70%	18.30%	0.00%	0.00%	NA
Japonica Intermediate	241	39.80%	60.20%	0.00%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	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
vg0123406476	T -> C	LOC_Os01g41370.1	upstream_gene_variant ; 2147.0bp to feature; MODIFIER	silent_mutation	Average:41.817; most accessible tissue: Callus, score: 69.373	N	N	N	N
vg0123406476	T -> C	LOC_Os01g41360.1	downstream_gene_variant ; 2354.0bp to feature; MODIFIER	silent_mutation	Average:41.817; most accessible tissue: Callus, score: 69.373	N	N	N	N
vg0123406476	T -> C	LOC_Os01g41360-LOC_Os01g41370	intergenic_region ; MODIFIER	silent_mutation	Average:41.817; most accessible tissue: Callus, score: 69.373	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123406476	9.37E-07	NA	mr1071	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
vg0123406476	NA	1.39E-06	mr1078	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
vg0123406476	4.35E-06	NA	mr1140	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
vg0123406476	NA	7.26E-08	mr1193	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
vg0123406476	NA	9.13E-06	mr1202	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
vg0123406476	5.11E-06	NA	mr1203	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
vg0123406476	NA	1.72E-06	mr1359	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
vg0123406476	NA	1.88E-06	mr1359	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
vg0123406476	NA	7.00E-06	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
vg0123406476	NA	8.58E-06	mr1441	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
vg0123406476	1.00E-06	NA	mr1467	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
vg0123406476	1.73E-06	NA	mr1618	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
vg0123406476	NA	2.97E-06	mr1837	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