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Detailed information for vg0514534980:

Variant ID: vg0514534980 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14534980
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGAATCATGCTATACAAAAGGTAAAGCCGTTGCCCATACTGGCTTGTGGTTGGCACGGTTAATGTTTCACAACAGTAGCTCCCGAACCGGTCCTTAATT[A/G]
TCACGAGCGCCACCATCAAAACCATATACTCACAACCCACCTTTAATCAGGTTTTAATTATCAATTAATTATCATAACACGATTAGCCATCGTGAGCTAC

Reverse complement sequence

GTAGCTCACGATGGCTAATCGTGTTATGATAATTAATTGATAATTAAAACCTGATTAAAGGTGGGTTGTGAGTATATGGTTTTGATGGTGGCGCTCGTGA[T/C]
AATTAAGGACCGGTTCGGGAGCTACTGTTGTGAAACATTAACCGTGCCAACCACAAGCCAGTATGGGCAACGGCTTTACCTTTTGTATAGCATGATTCAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.00%	0.30%	12.82%	44.90%	NA
All Indica	2759	11.30%	0.40%	16.85%	71.40%	NA
All Japonica	1512	97.60%	0.00%	0.86%	1.59%	NA
Aus	269	19.30%	0.70%	44.98%	34.94%	NA
Indica I	595	14.50%	0.20%	17.48%	67.90%	NA
Indica II	465	6.70%	0.00%	10.32%	83.01%	NA
Indica III	913	10.30%	0.70%	22.45%	66.59%	NA
Indica Intermediate	786	12.80%	0.60%	13.74%	72.77%	NA
Temperate Japonica	767	97.50%	0.00%	0.13%	2.35%	NA
Tropical Japonica	504	97.00%	0.00%	2.18%	0.79%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	55.60%	0.00%	6.67%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0514534980	A -> DEL	N	N	silent_mutation	Average:22.761; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N
vg0514534980	A -> G	LOC_Os05g25100.1	downstream_gene_variant ; 346.0bp to feature; MODIFIER	silent_mutation	Average:22.761; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N
vg0514534980	A -> G	LOC_Os05g25090-LOC_Os05g25100	intergenic_region ; MODIFIER	silent_mutation	Average:22.761; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514534980	1.30E-09	1.30E-09	mr1460	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
vg0514534980	NA	6.74E-18	mr1336_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