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Detailed information for vg0505835605:

Variant ID: vg0505835605 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5835605
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATGCCCTGCTACCAACCGGGACTAAAGATCCCTTCGTCCCGTTGAAGTAATAAACCGGGACTAATAAGCCACTTTAGTCCCGGTTCGTTTTGAAACCG[A/G]
GACTATTGTGGAAATCGGCCGACCCTCCAAAGACCTCTTCTCCAGCAGTAGTGGATATTTCTTAGTGGTAACAAACATAGGTCTCTAGGTATTCTATCTG

Reverse complement sequence

CAGATAGAATACCTAGAGACCTATGTTTGTTACCACTAAGAAATATCCACTACTGCTGGAGAAGAGGTCTTTGGAGGGTCGGCCGATTTCCACAATAGTC[T/C]
CGGTTTCAAAACGAACCGGGACTAAAGTGGCTTATTAGTCCCGGTTTATTACTTCAACGGGACGAAGGGATCTTTAGTCCCGGTTGGTAGCAGGGCATGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.80%	25.90%	0.25%	0.04%	NA
All Indica	2759	81.00%	18.50%	0.40%	0.07%	NA
All Japonica	1512	60.50%	39.40%	0.07%	0.00%	NA
Aus	269	92.60%	7.40%	0.00%	0.00%	NA
Indica I	595	75.80%	23.50%	0.67%	0.00%	NA
Indica II	465	93.30%	5.80%	0.86%	0.00%	NA
Indica III	913	79.60%	20.20%	0.11%	0.11%	NA
Indica Intermediate	786	79.30%	20.40%	0.25%	0.13%	NA
Temperate Japonica	767	38.10%	61.90%	0.00%	0.00%	NA
Tropical Japonica	504	94.20%	5.80%	0.00%	0.00%	NA
Japonica Intermediate	241	61.40%	38.20%	0.41%	0.00%	NA
VI/Aromatic	96	22.90%	77.10%	0.00%	0.00%	NA
Intermediate	90	72.20%	27.80%	0.00%	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
vg0505835605	A -> DEL	N	N	silent_mutation	Average:48.365; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0505835605	A -> G	LOC_Os05g10660.1	upstream_gene_variant ; 774.0bp to feature; MODIFIER	silent_mutation	Average:48.365; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0505835605	A -> G	LOC_Os05g10660-LOC_Os05g10670	intergenic_region ; MODIFIER	silent_mutation	Average:48.365; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505835605	NA	2.19E-08	mr1550_2	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
vg0505835605	NA	1.82E-06	mr1672_2	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
vg0505835605	NA	9.51E-06	mr1713_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