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Detailed information for vg0414370101:

Variant ID: vg0414370101 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14370101
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAGAGGAGGGATCAACAACATGTCGATATAGTGACACAATCGATCAGAAAAGTACCGGGTACAGTCTACAAGAGCTGCTCTATGCTGTGAACTACCCA[T/C]
GTCTAGTTTGGTAGAGCATCTCCAGTGTGGGGCTAGCATCGATTTTAGAGGAAAGAAACCGAACAATGCACATTGTTAGAATCGATTAGATTGTGTTCGG

Reverse complement sequence

CCGAACACAATCTAATCGATTCTAACAATGTGCATTGTTCGGTTTCTTTCCTCTAAAATCGATGCTAGCCCCACACTGGAGATGCTCTACCAAACTAGAC[A/G]
TGGGTAGTTCACAGCATAGAGCAGCTCTTGTAGACTGTACCCGGTACTTTTCTGATCGATTGTGTCACTATATCGACATGTTGTTGATCCCTCCTCTGAA

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	72.70%	20.90%	1.42%	5.04%	NA
All Indica	2759	87.60%	6.20%	1.96%	4.28%	NA
All Japonica	1512	41.30%	50.90%	0.53%	7.28%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	70.80%	15.30%	0.84%	13.11%	NA
Indica II	465	95.50%	3.70%	0.43%	0.43%	NA
Indica III	913	92.80%	2.50%	3.40%	1.31%	NA
Indica Intermediate	786	89.60%	5.10%	2.04%	3.31%	NA
Temperate Japonica	767	6.80%	84.70%	0.65%	7.82%	NA
Tropical Japonica	504	86.50%	6.00%	0.40%	7.14%	NA
Japonica Intermediate	241	56.80%	36.90%	0.41%	5.81%	NA
VI/Aromatic	96	76.00%	14.60%	4.17%	5.21%	NA
Intermediate	90	60.00%	33.30%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414370101	T -> C	LOC_Os04g24940.1	downstream_gene_variant ; 3592.0bp to feature; MODIFIER	silent_mutation	Average:15.398; most accessible tissue: Callus, score: 38.711	N	N	N	N
vg0414370101	T -> C	LOC_Os04g24950.1	downstream_gene_variant ; 621.0bp to feature; MODIFIER	silent_mutation	Average:15.398; most accessible tissue: Callus, score: 38.711	N	N	N	N
vg0414370101	T -> C	LOC_Os04g24940-LOC_Os04g24950	intergenic_region ; MODIFIER	silent_mutation	Average:15.398; most accessible tissue: Callus, score: 38.711	N	N	N	N
vg0414370101	T -> DEL	N	N	silent_mutation	Average:15.398; most accessible tissue: Callus, score: 38.711	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414370101	NA	2.21E-06	mr1330	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
vg0414370101	NA	1.27E-06	mr1403	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
vg0414370101	NA	7.19E-10	mr1549	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
vg0414370101	NA	1.65E-06	mr1570	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
vg0414370101	NA	5.88E-08	mr1757	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
vg0414370101	NA	9.08E-08	mr1864	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