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Detailed information for vg0523036172:

Variant ID: vg0523036172 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23036172
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:

TTCACCTCATCAGCTGCAGCATCATCGGCTACGGGAACCTAATTCTTGACACGCCACTCCTGTCATGGCTTTGGTTTCCTCAGCCGATGGTTGATTTCCT[T/C]
CTCAACCTCCTGAAAACGCTCCCTGCTCCTCAATCTCTGGACCCTCCTCTTCTGATTCTTCGTGAAAATATCAGAAGGACACCATTGATTCTTCCTGATC

Reverse complement sequence

GATCAGGAAGAATCAATGGTGTCCTTCTGATATTTTCACGAAGAATCAGAAGAGGAGGGTCCAGAGATTGAGGAGCAGGGAGCGTTTTCAGGAGGTTGAG[A/G]
AGGAAATCAACCATCGGCTGAGGAAACCAAAGCCATGACAGGAGTGGCGTGTCAAGAATTAGGTTCCCGTAGCCGATGATGCTGCAGCTGATGAGGTGAA

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	65.90%	34.00%	0.08%	0.00%	NA
All Indica	2759	98.90%	1.10%	0.07%	0.00%	NA
All Japonica	1512	1.40%	98.60%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.00%	0.80%	0.17%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	98.10%	1.90%	0.00%	0.00%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	2.00%	98.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	42.70%	56.20%	1.04%	0.00%	NA
Intermediate	90	63.30%	35.60%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0523036172	T -> C	LOC_Os05g39270.1	downstream_gene_variant ; 1996.0bp to feature; MODIFIER	silent_mutation	Average:22.728; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0523036172	T -> C	LOC_Os05g39290.1	downstream_gene_variant ; 1999.0bp to feature; MODIFIER	silent_mutation	Average:22.728; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0523036172	T -> C	LOC_Os05g39280.1	intron_variant ; MODIFIER	silent_mutation	Average:22.728; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523036172	NA	5.34E-31	mr1243	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
vg0523036172	NA	8.34E-12	mr1626	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
vg0523036172	NA	2.52E-28	mr1631	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
vg0523036172	6.97E-06	NA	mr1879	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
vg0523036172	NA	5.71E-12	mr1258_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
vg0523036172	NA	7.35E-15	mr1767_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