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Detailed information for vg0918882956:

Variant ID: vg0918882956 (JBrowse)	Variation Type: INDEL
Chromosome: chr09	Position: 18882956
Reference Allele: T	Alternative Allele: A,TA,TAAA,TAAAA,TAA
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, T: 0.18, others allele: 0.00, population size: 91. )

Flanking Sequence (100 bp) in Reference Genome:

AACATTAGTTGTTTTTAGTTTTTTAGGTAAGAGAACTACAGAAGACACTCCATGGCTCTTATTCAGCGTATAAACGCTTTCTTGGACTTCTTTTTTTTTT[T/A,TA,TAAA,TAAAA,TAA]
AAAAAAAAAGCAAGCAGGATTGCAAACAGATTCTACAAATTGGAAAATGTACCAGTCATACAAAATGTCCAGCAGGACAAGCTATCATAGTATCATACAG

Reverse complement sequence

CTGTATGATACTATGATAGCTTGTCCTGCTGGACATTTTGTATGACTGGTACATTTTCCAATTTGTAGAATCTGTTTGCAATCCTGCTTGCTTTTTTTTT[A/T,TA,TTTA,TTTTA,TTA]
AAAAAAAAAAGAAGTCCAAGAAAGCGTTTATACGCTGAATAAGAGCCATGGAGTGTCTTCTGTAGTTCTCTTACCTAAAAAACTAAAAACAACTAATGTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.00%	27.30%	1.97%	0.00%	TA: 3.60%; TAAAA: 0.76%; TAAA: 0.40%; TAA: 0.02%
All Indica	2759	90.80%	3.10%	0.62%	0.00%	TA: 4.78%; TAAA: 0.69%
All Japonica	1512	18.00%	75.00%	4.63%	0.00%	TAAAA: 2.12%; TA: 0.20%; TAA: 0.07%
Aus	269	82.20%	5.60%	0.74%	0.00%	TA: 11.15%; TAAAA: 0.37%
Indica I	595	87.70%	1.80%	2.02%	0.00%	TA: 8.24%; TAAA: 0.17%
Indica II	465	96.10%	3.40%	0.00%	0.00%	TA: 0.43%
Indica III	913	92.90%	2.80%	0.33%	0.00%	TA: 2.63%; TAAA: 1.31%
Indica Intermediate	786	87.70%	4.10%	0.25%	0.00%	TA: 7.25%; TAAA: 0.76%
Temperate Japonica	767	18.10%	75.00%	5.61%	0.00%	TAAAA: 1.17%; TAA: 0.13%
Tropical Japonica	504	15.90%	79.20%	3.37%	0.00%	TAAAA: 0.99%; TA: 0.60%
Japonica Intermediate	241	22.00%	66.40%	4.15%	0.00%	TAAAA: 7.47%
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	43.30%	43.30%	4.44%	0.00%	TA: 5.56%; TAAAA: 3.33%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0918882956	T -> TAA	LOC_Os09g31400.1	3_prime_UTR_variant ; 1052.0bp to feature; MODIFIER	silent_mutation	Average:56.166; most accessible tissue: Minghui63 root, score: 70.332	N	N	N	N
vg0918882956	T -> TAAAA	LOC_Os09g31400.1	3_prime_UTR_variant ; 1052.0bp to feature; MODIFIER	silent_mutation	Average:56.166; most accessible tissue: Minghui63 root, score: 70.332	N	N	N	N
vg0918882956	T -> A	LOC_Os09g31400.1	3_prime_UTR_variant ; 1053.0bp to feature; MODIFIER	silent_mutation	Average:56.166; most accessible tissue: Minghui63 root, score: 70.332	N	N	N	N
vg0918882956	T -> TAAA	LOC_Os09g31400.1	3_prime_UTR_variant ; 1052.0bp to feature; MODIFIER	silent_mutation	Average:56.166; most accessible tissue: Minghui63 root, score: 70.332	N	N	N	N
vg0918882956	T -> TA	LOC_Os09g31400.1	3_prime_UTR_variant ; 1052.0bp to feature; MODIFIER	silent_mutation	Average:56.166; most accessible tissue: Minghui63 root, score: 70.332	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0918882956	NA	3.86E-08	mr1246	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
vg0918882956	NA	6.00E-06	mr1246	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
vg0918882956	NA	6.93E-06	mr1404	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
vg0918882956	1.34E-06	7.11E-07	mr1517	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
vg0918882956	4.84E-06	1.80E-07	mr1538	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
vg0918882956	NA	3.41E-19	mr1598	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
vg0918882956	NA	9.38E-11	mr1246_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
vg0918882956	NA	1.82E-07	mr1399_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