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Detailed information for vg1124331154:

Variant ID: vg1124331154 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24331154
Reference Allele: T	Alternative Allele: C,A
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.06, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

ATATAGCGTAGACACGCAGGGAGATGATGGCGACGTGGCCATGGACTCGTAGCGACTAGGAGCTATATTGGTTTGAGAGGAGTGCCCATAATCAGAGCCC[T/C,A]
GGGGAAGTAGGCTTCGGTTGAACCTTGTTAACAAATATCGTGTGTTCCTGTGTCGTTATCTGACGTGTCTTAGGTGATCAATGACTAAATCGATCAAGAA

Reverse complement sequence

TTCTTGATCGATTTAGTCATTGATCACCTAAGACACGTCAGATAACGACACAGGAACACACGATATTTGTTAACAAGGTTCAACCGAAGCCTACTTCCCC[A/G,T]
GGGCTCTGATTATGGGCACTCCTCTCAAACCAATATAGCTCCTAGTCGCTACGAGTCCATGGCCACGTCGCCATCATCTCCCTGCGTGTCTACGCTATAT

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	63.50%	34.40%	0.55%	1.50%	A: 0.04%
All Indica	2759	44.70%	54.10%	0.40%	0.80%	NA
All Japonica	1512	97.40%	2.60%	0.00%	0.07%	NA
Aus	269	68.00%	9.70%	4.83%	17.47%	NA
Indica I	595	50.90%	48.90%	0.17%	0.00%	NA
Indica II	465	58.30%	40.40%	0.65%	0.65%	NA
Indica III	913	26.80%	72.00%	0.22%	0.99%	NA
Indica Intermediate	786	52.70%	45.40%	0.64%	1.27%	NA
Temperate Japonica	767	98.20%	1.80%	0.00%	0.00%	NA
Tropical Japonica	504	96.00%	3.80%	0.00%	0.20%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	49.00%	51.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	18.90%	2.22%	1.11%	A: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124331154	T -> A	LOC_Os11g40700-LOC_Os11g40720	intergenic_region ; MODIFIER	silent_mutation	Average:46.914; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N
vg1124331154	T -> DEL	N	N	silent_mutation	Average:46.914; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N
vg1124331154	T -> C	LOC_Os11g40700-LOC_Os11g40720	intergenic_region ; MODIFIER	silent_mutation	Average:46.914; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124331154	4.22E-06	3.74E-07	mr1133	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