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Detailed information for vg0414197719:

Variant ID: vg0414197719 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14197719
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TTACATAAATGTGGAACTAGTTCAGTATTTATAAATGATGTGCAACTGGTTCATTATTTCTAACAAATGTGCATCTTGTTAAATACTCTTAATAAATGTG[T/C]
AACTGGTTAAATAATTTTAATTGCCTTGATTATTTGTGGAACAGGCGGAATTTGTTGAGCATGTTCACGTGGAGTCCGACACCCTACTGCAAAGACTAGA

Reverse complement sequence

TCTAGTCTTTGCAGTAGGGTGTCGGACTCCACGTGAACATGCTCAACAAATTCCGCCTGTTCCACAAATAATCAAGGCAATTAAAATTATTTAACCAGTT[A/G]
CACATTTATTAAGAGTATTTAACAAGATGCACATTTGTTAGAAATAATGAACCAGTTGCACATCATTTATAAATACTGAACTAGTTCCACATTTATGTAA

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	13.80%	11.80%	4.89%	69.47%	NA
All Indica	2759	7.40%	4.30%	3.23%	85.07%	NA
All Japonica	1512	28.20%	21.20%	5.62%	44.91%	NA
Aus	269	0.40%	37.90%	7.43%	54.28%	NA
Indica I	595	23.50%	9.40%	3.70%	63.36%	NA
Indica II	465	0.90%	1.70%	3.01%	94.41%	NA
Indica III	913	1.60%	3.20%	2.63%	92.55%	NA
Indica Intermediate	786	5.70%	3.30%	3.69%	87.28%	NA
Temperate Japonica	767	46.00%	40.20%	7.17%	6.65%	NA
Tropical Japonica	504	2.40%	0.20%	1.59%	95.83%	NA
Japonica Intermediate	241	25.70%	5.00%	9.13%	60.17%	NA
VI/Aromatic	96	9.40%	6.20%	31.25%	53.12%	NA
Intermediate	90	13.30%	12.20%	7.78%	66.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414197719	T -> C	LOC_Os04g24730.1	intron_variant ; MODIFIER	silent_mutation	Average:7.253; most accessible tissue: Callus, score: 18.519	N	N	N	N
vg0414197719	T -> DEL	N	N	silent_mutation	Average:7.253; most accessible tissue: Callus, score: 18.519	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414197719	NA	8.63E-09	mr1054	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
vg0414197719	NA	2.90E-07	mr1062	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
vg0414197719	NA	4.44E-08	mr1287	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
vg0414197719	NA	2.79E-07	mr1328	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
vg0414197719	NA	3.56E-06	mr1345	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
vg0414197719	NA	6.35E-06	mr1353	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
vg0414197719	NA	5.21E-08	mr1372	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
vg0414197719	NA	9.37E-07	mr1400	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
vg0414197719	NA	1.94E-09	mr1403	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
vg0414197719	NA	7.29E-06	mr1427	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
vg0414197719	NA	2.75E-07	mr1432	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
vg0414197719	NA	7.30E-06	mr1433	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
vg0414197719	NA	2.41E-07	mr1512	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
vg0414197719	NA	9.47E-06	mr1525	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
vg0414197719	NA	2.61E-07	mr1545	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
vg0414197719	NA	2.29E-08	mr1585	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
vg0414197719	NA	7.30E-07	mr1596	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
vg0414197719	NA	1.76E-06	mr1634	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
vg0414197719	NA	3.83E-06	mr1774	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
vg0414197719	NA	1.74E-11	mr1927	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
vg0414197719	NA	2.54E-07	mr1582_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