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Detailed information for vg0420961717:

Variant ID: vg0420961717 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20961717
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACTTGCCGGTAACGACGTTTGCACCAGGTGGGCGAGGGACGAGCCGCCACGTGCCGTTGTCGATCAAAGCCTTGAACTCTTCGGCCATGGCTGCACGC[T/C]
AGTTGGGGTCGGCGAGGGCAGAGCGGTAGTTGGCCGGCAGTGGAGAAATGGCGCCGTGGGATGCCGAGAGCACGAGTCGATCCATTGGCTTGAGAGAATC

Reverse complement sequence

GATTCTCTCAAGCCAATGGATCGACTCGTGCTCTCGGCATCCCACGGCGCCATTTCTCCACTGCCGGCCAACTACCGCTCTGCCCTCGCCGACCCCAACT[A/G]
GCGTGCAGCCATGGCCGAAGAGTTCAAGGCTTTGATCGACAACGGCACGTGGCGGCTCGTCCCTCGCCCACCTGGTGCAAACGTCGTTACCGGCAAGTGG

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	84.20%	8.60%	3.15%	4.04%	NA
All Indica	2759	90.10%	6.40%	1.27%	2.21%	NA
All Japonica	1512	85.30%	0.70%	7.14%	6.88%	NA
Aus	269	26.00%	74.00%	0.00%	0.00%	NA
Indica I	595	96.60%	0.00%	3.36%	0.00%	NA
Indica II	465	96.10%	3.00%	0.65%	0.22%	NA
Indica III	913	83.50%	10.60%	0.55%	5.37%	NA
Indica Intermediate	786	89.40%	8.30%	0.89%	1.40%	NA
Temperate Japonica	767	87.00%	0.00%	10.30%	2.74%	NA
Tropical Japonica	504	80.40%	1.60%	4.37%	13.69%	NA
Japonica Intermediate	241	90.00%	1.20%	2.90%	5.81%	NA
VI/Aromatic	96	63.50%	10.40%	3.12%	22.92%	NA
Intermediate	90	81.10%	11.10%	3.33%	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
vg0420961717	T -> C	LOC_Os04g34640.1	upstream_gene_variant ; 3367.0bp to feature; MODIFIER	silent_mutation	Average:56.435; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0420961717	T -> C	LOC_Os04g34650.1	intron_variant ; MODIFIER	silent_mutation	Average:56.435; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0420961717	T -> DEL	N	N	silent_mutation	Average:56.435; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420961717	9.20E-07	NA	mr1946_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
vg0420961717	9.20E-07	NA	mr1948_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