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Detailed information for vg1010284480:

Variant ID: vg1010284480 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10284480
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTAAGTGAAACGGTGGATCAGTTTGTGACGAGGACATCCCTTCCAACGATACAACCACGCCTATTGCACAGCAAGGACCAATGACTAGAGCTCGAGCTC[A/G]
TGAACTTAATTATCAGGTAAAGTCATTCCTAGCTAATCATACAAGTTCTTCTCAGAATTGGGTGCTACTAAATGGTTGTTGTGATCTACTTGTTGTTAGG

Reverse complement sequence

CCTAACAACAAGTAGATCACAACAACCATTTAGTAGCACCCAATTCTGAGAAGAACTTGTATGATTAGCTAGGAATGACTTTACCTGATAATTAAGTTCA[T/C]
GAGCTCGAGCTCTAGTCATTGGTCCTTGCTGTGCAATAGGCGTGGTTGTATCGTTGGAAGGGATGTCCTCGTCACAAACTGATCCACCGTTTCACTTAAA

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	22.10%	0.60%	11.51%	65.79%	NA
All Indica	2759	1.70%	0.00%	4.53%	93.80%	NA
All Japonica	1512	63.80%	1.80%	4.10%	30.29%	NA
Aus	269	3.00%	0.00%	94.42%	2.60%	NA
Indica I	595	0.80%	0.00%	2.69%	96.47%	NA
Indica II	465	1.90%	0.00%	1.94%	96.13%	NA
Indica III	913	2.10%	0.00%	3.94%	93.98%	NA
Indica Intermediate	786	1.70%	0.00%	8.14%	90.20%	NA
Temperate Japonica	767	81.20%	3.40%	2.87%	12.52%	NA
Tropical Japonica	504	37.50%	0.00%	5.75%	56.75%	NA
Japonica Intermediate	241	63.50%	0.40%	4.56%	31.54%	NA
VI/Aromatic	96	0.00%	0.00%	83.33%	16.67%	NA
Intermediate	90	30.00%	0.00%	25.56%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1010284480	A -> G	LOC_Os10g20440.1	upstream_gene_variant ; 1920.0bp to feature; MODIFIER	silent_mutation	Average:23.748; most accessible tissue: Minghui63 root, score: 46.493	N	N	N	N
vg1010284480	A -> G	LOC_Os10g20430-LOC_Os10g20440	intergenic_region ; MODIFIER	silent_mutation	Average:23.748; most accessible tissue: Minghui63 root, score: 46.493	N	N	N	N
vg1010284480	A -> DEL	N	N	silent_mutation	Average:23.748; most accessible tissue: Minghui63 root, score: 46.493	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010284480	NA	9.94E-06	mr1519_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
vg1010284480	1.14E-06	NA	mr1676_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