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Detailed information for vg0133875165:

Variant ID: vg0133875165 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 33875165
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTTCTTTAAACTTTTACCTTTTTCGTCACGTCGAACTTTCCTACACACACAAACTTCCAACTTTTCCGTCATATCGTTCCAATTTCTTCAAACTTT[C/T]
AATTTTAGCGTGGAACTAAACGCAACCTAATTTATTCGGTTTCTATTACACCGTATATATTCTATGGGAAACAAAGTGCAATTTATACAAACTTGTATTA

Reverse complement sequence

TAATACAAGTTTGTATAAATTGCACTTTGTTTCCCATAGAATATATACGGTGTAATAGAAACCGAATAAATTAGGTTGCGTTTAGTTCCACGCTAAAATT[G/A]
AAAGTTTGAAGAAATTGGAACGATATGACGGAAAAGTTGGAAGTTTGTGTGTGTAGGAAAGTTCGACGTGACGAAAAAGGTAAAAGTTTAAAGAAAAAAA

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	94.50%	5.40%	0.08%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	83.90%	15.90%	0.26%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	85.40%	14.30%	0.26%	0.00%	NA
Tropical Japonica	504	85.90%	13.90%	0.20%	0.00%	NA
Japonica Intermediate	241	74.70%	24.90%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0133875165	C -> T	LOC_Os01g58580.1	downstream_gene_variant ; 3325.0bp to feature; MODIFIER	silent_mutation	Average:33.682; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0133875165	C -> T	LOC_Os01g58590.1	downstream_gene_variant ; 1434.0bp to feature; MODIFIER	silent_mutation	Average:33.682; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0133875165	C -> T	LOC_Os01g58580-LOC_Os01g58590	intergenic_region ; MODIFIER	silent_mutation	Average:33.682; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0133875165	2.51E-06	NA	mr1720	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