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Detailed information for vg0514857972:

Variant ID: vg0514857972 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14857972
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAACGAGCCAGCACTCTAAGGCCCAAGCCCAACAAACAATGAGACAACACAAGTTACTCAACGGCCCAAGCCCAACTGAAAGGAAAACCCTAGAGACTAC[C/T]
CTCGGTCTCCCACTCTCCCCGATTTCCCTGTCTCCCGCATCCTGCCATTCCTGCGCCGCATGCCCGCATCATGCGCCGCCAATCCCCTTTCACACCGGCG

Reverse complement sequence

CGCCGGTGTGAAAGGGGATTGGCGGCGCATGATGCGGGCATGCGGCGCAGGAATGGCAGGATGCGGGAGACAGGGAAATCGGGGAGAGTGGGAGACCGAG[G/A]
GTAGTCTCTAGGGTTTTCCTTTCAGTTGGGCTTGGGCCGTTGAGTAACTTGTGTTGTCTCATTGTTTGTTGGGCTTGGGCCTTAGAGTGCTGGCTCGTTA

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	82.80%	13.10%	4.17%	0.00%	NA
All Indica	2759	98.00%	0.80%	1.16%	0.00%	NA
All Japonica	1512	51.80%	38.20%	9.99%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.80%	2.50%	1.68%	0.00%	NA
Indica II	465	97.00%	0.90%	2.15%	0.00%	NA
Indica III	913	99.70%	0.10%	0.22%	0.00%	NA
Indica Intermediate	786	98.50%	0.30%	1.27%	0.00%	NA
Temperate Japonica	767	19.70%	69.00%	11.34%	0.00%	NA
Tropical Japonica	504	92.50%	0.80%	6.75%	0.00%	NA
Japonica Intermediate	241	68.90%	18.70%	12.45%	0.00%	NA
VI/Aromatic	96	86.50%	3.10%	10.42%	0.00%	NA
Intermediate	90	80.00%	15.60%	4.44%	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
vg0514857972	C -> T	LOC_Os05g25560.1	upstream_gene_variant ; 1678.0bp to feature; MODIFIER	silent_mutation	Average:70.452; most accessible tissue: Zhenshan97 young leaf, score: 86.852	N	N	N	N
vg0514857972	C -> T	LOC_Os05g25570.1	upstream_gene_variant ; 147.0bp to feature; MODIFIER	silent_mutation	Average:70.452; most accessible tissue: Zhenshan97 young leaf, score: 86.852	N	N	N	N
vg0514857972	C -> T	LOC_Os05g25560-LOC_Os05g25570	intergenic_region ; MODIFIER	silent_mutation	Average:70.452; most accessible tissue: Zhenshan97 young leaf, score: 86.852	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514857972	NA	1.93E-08	mr1552	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
vg0514857972	4.07E-06	NA	mr1757	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