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Detailed information for vg0414330196:

Variant ID: vg0414330196 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14330196
Reference Allele: C	Alternative Allele: T
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: 104. )

Flanking Sequence (100 bp) in Reference Genome:

GATCAGGGGGCGGCTAACAACGCGCGTAAGGACGTGATGGAAGAAGTCAGTGATCTAGGAGAGTCTGTTCTCCCACTTTTTGAAGAGTAGGACTTCAGTT[C/T]
GGCTGTACTCCTTAATCAATTATGCTTTGTAAAACTTTTGTCGGTTCCAACTGCCTTTGTGTGTGCAGTCATTACCTTAGTTTTCTTTAGCATTTTGATT

Reverse complement sequence

AATCAAAATGCTAAAGAAAACTAAGGTAATGACTGCACACACAAAGGCAGTTGGAACCGACAAAAGTTTTACAAAGCATAATTGATTAAGGAGTACAGCC[G/A]
AACTGAAGTCCTACTCTTCAAAAAGTGGGAGAACAGACTCTCCTAGATCACTGACTTCTTCCATCACGTCCTTACGCGCGTTGTTAGCCGCCCCCTGATC

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	62.70%	21.20%	3.87%	12.25%	NA
All Indica	2759	49.10%	31.10%	4.13%	15.69%	NA
All Japonica	1512	89.90%	2.70%	2.05%	5.29%	NA
Aus	269	47.20%	25.70%	8.18%	18.96%	NA
Indica I	595	50.10%	38.20%	3.03%	8.74%	NA
Indica II	465	33.30%	42.20%	5.59%	18.92%	NA
Indica III	913	61.20%	16.00%	4.38%	18.40%	NA
Indica Intermediate	786	43.60%	36.60%	3.82%	15.90%	NA
Temperate Japonica	767	91.50%	0.40%	1.56%	6.52%	NA
Tropical Japonica	504	90.30%	6.50%	1.59%	1.59%	NA
Japonica Intermediate	241	84.20%	2.10%	4.56%	9.13%	NA
VI/Aromatic	96	62.50%	19.80%	12.50%	5.21%	NA
Intermediate	90	66.70%	17.80%	4.44%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414330196	C -> DEL	N	N	silent_mutation	Average:10.458; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0414330196	C -> T	LOC_Os04g24870.1	downstream_gene_variant ; 1513.0bp to feature; MODIFIER	silent_mutation	Average:10.458; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0414330196	C -> T	LOC_Os04g24880.1	downstream_gene_variant ; 3083.0bp to feature; MODIFIER	silent_mutation	Average:10.458; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0414330196	C -> T	LOC_Os04g24860.1	intron_variant ; MODIFIER	silent_mutation	Average:10.458; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414330196	NA	4.14E-06	mr1181	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