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Detailed information for vg0430897454:

Variant ID: vg0430897454 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30897454
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TATTACATGAATATATTGTGTACACAGCACTGGTCCCCAATTCCCACCTTCATGCTAGATATTTTTAAAGACTACATAAATAAATTCATGAGACTTCAAA[T/C]
TTCTTTCGTCAGACAGACACGTCACTAATTGTTACAGGTTCCAGCAGACAGCCATCACATATTATAGCTACATACAATACACTGAAACCAGCAATTTTAT

Reverse complement sequence

ATAAAATTGCTGGTTTCAGTGTATTGTATGTAGCTATAATATGTGATGGCTGTCTGCTGGAACCTGTAACAATTAGTGACGTGTCTGTCTGACGAAAGAA[A/G]
TTTGAAGTCTCATGAATTTATTTATGTAGTCTTTAAAAATATCTAGCATGAAGGTGGGAATTGGGGACCAGTGCTGTGTACACAATATATTCATGTAATA

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	82.30%	17.70%	0.00%	0.00%	NA
All Indica	2759	76.60%	23.40%	0.00%	0.00%	NA
All Japonica	1512	89.20%	10.80%	0.00%	0.00%	NA
Aus	269	92.20%	7.80%	0.00%	0.00%	NA
Indica I	595	88.40%	11.60%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	55.20%	44.80%	0.00%	0.00%	NA
Indica Intermediate	786	80.50%	19.50%	0.00%	0.00%	NA
Temperate Japonica	767	96.10%	3.90%	0.00%	0.00%	NA
Tropical Japonica	504	94.60%	5.40%	0.00%	0.00%	NA
Japonica Intermediate	241	56.00%	44.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0430897454	T -> C	LOC_Os04g52020.1	intron_variant ; MODIFIER	silent_mutation	Average:52.926; most accessible tissue: Callus, score: 73.206	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430897454	NA	2.34E-06	mr1534	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
vg0430897454	8.96E-07	7.68E-11	mr1745	Jap_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
vg0430897454	NA	6.24E-08	mr1745_2	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