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Detailed information for vg0421518167:

Variant ID: vg0421518167 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21518167
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

ATCCAGTCCTTTTCTCCACCGAAACTGGTGTGGAAACTGGATGAGAAAAAACAGTATCTTCCTTTGTTCCCTTCCATCTAATAATATTTCCCATCCAACA[T/C]
ATTCTGAGTGCAGTTATGCAATGTTGTCTGTTGCAGTTTGTATTGACTGCTGCAGGTACCCAAGCAGAAAAAGTAATTGATCAACTGAAACCTTCGCATG

Reverse complement sequence

CATGCGAAGGTTTCAGTTGATCAATTACTTTTTCTGCTTGGGTACCTGCAGCAGTCAATACAAACTGCAACAGACAACATTGCATAACTGCACTCAGAAT[A/G]
TGTTGGATGGGAAATATTATTAGATGGAAGGGAACAAAGGAAGATACTGTTTTTTCTCATCCAGTTTCCACACCAGTTTCGGTGGAGAAAAGGACTGGAT

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	84.10%	15.60%	0.17%	0.11%	NA
All Indica	2759	74.20%	25.40%	0.25%	0.14%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	82.90%	17.00%	0.17%	0.00%	NA
Indica II	465	78.10%	21.90%	0.00%	0.00%	NA
Indica III	913	63.20%	36.70%	0.11%	0.00%	NA
Indica Intermediate	786	78.00%	20.90%	0.64%	0.51%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	87.80%	11.10%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0421518167	T -> C	LOC_Os04g35380.4	3_prime_UTR_variant ; 1919.0bp to feature; MODIFIER	silent_mutation	Average:59.863; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N
vg0421518167	T -> C	LOC_Os04g35380.2	3_prime_UTR_variant ; 1109.0bp to feature; MODIFIER	silent_mutation	Average:59.863; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N
vg0421518167	T -> C	LOC_Os04g35380.1	intron_variant ; MODIFIER	silent_mutation	Average:59.863; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N
vg0421518167	T -> C	LOC_Os04g35380.5	intron_variant ; MODIFIER	silent_mutation	Average:59.863; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N
vg0421518167	T -> DEL	N	N	silent_mutation	Average:59.863; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421518167	NA	4.95E-07	mr1317_2	Ind_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
vg0421518167	NA	7.16E-07	mr1610_2	Ind_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
vg0421518167	NA	4.44E-06	mr1818_2	Ind_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
vg0421518167	6.27E-07	2.05E-07	mr1897_2	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