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Detailed information for vg0421189516:

Variant ID: vg0421189516 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21189516
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATAATATCTATGTGCAGTTTAGTTCTAATTTACCGGCTATTCTCACACGTTGGCTTTTTTTATTGACTGAGATATCATTTTCACTACAGTCCAAATGTG[T/C]
TGGTCAATTCATAATCGATCAGCAGGCCTGGAATTTGTCTCAAGGTATATACATGGAATAGTGTTCCAATATGAGTAGTGACTAAAGCAGATTAATTTGA

Reverse complement sequence

TCAAATTAATCTGCTTTAGTCACTACTCATATTGGAACACTATTCCATGTATATACCTTGAGACAAATTCCAGGCCTGCTGATCGATTATGAATTGACCA[A/G]
CACATTTGGACTGTAGTGAAAATGATATCTCAGTCAATAAAAAAAGCCAACGTGTGAGAATAGCCGGTAAATTAGAACTAAACTGCACATAGATATTATA

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	63.90%	0.10%	2.16%	33.79%	NA
All Indica	2759	48.50%	0.20%	2.97%	48.39%	NA
All Japonica	1512	97.50%	0.00%	0.26%	2.25%	NA
Aus	269	31.60%	0.40%	3.35%	64.68%	NA
Indica I	595	49.10%	0.00%	1.01%	49.92%	NA
Indica II	465	38.10%	0.40%	2.80%	58.71%	NA
Indica III	913	52.20%	0.20%	3.50%	44.03%	NA
Indica Intermediate	786	49.70%	0.10%	3.94%	46.18%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	93.80%	0.00%	0.79%	5.36%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	55.20%	0.00%	4.17%	40.62%	NA
Intermediate	90	80.00%	0.00%	3.33%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0421189516	T -> C	LOC_Os04g34890.1	upstream_gene_variant ; 3420.0bp to feature; MODIFIER	silent_mutation	Average:8.166; most accessible tissue: Callus, score: 14.102	N	N	N	N
vg0421189516	T -> C	LOC_Os04g34890-LOC_Os04g34900	intergenic_region ; MODIFIER	silent_mutation	Average:8.166; most accessible tissue: Callus, score: 14.102	N	N	N	N
vg0421189516	T -> DEL	N	N	silent_mutation	Average:8.166; most accessible tissue: Callus, score: 14.102	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421189516	7.34E-06	NA	mr1222_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
vg0421189516	3.44E-06	NA	mr1222_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