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Detailed information for vg1016644917:

Variant ID: vg1016644917 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 16644917
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGATTTGGATTTTAATTACTATAAACTTAAAAAATGGATTTATATGATATTTTTAAAGCAATTTCTATATAAAAAGTTTCACACAAAATACATCCTTT[G/A]
GCAGTTTGAAAAAACGTGTTAATGAAAACCGAGGTATAATCTGTATTTATCTTAATCTAGTTTGAACGGGGACTAATACTTTGACTTCACTTAATTATGC

Reverse complement sequence

GCATAATTAAGTGAAGTCAAAGTATTAGTCCCCGTTCAAACTAGATTAAGATAAATACAGATTATACCTCGGTTTTCATTAACACGTTTTTTCAAACTGC[C/T]
AAAGGATGTATTTTGTGTGAAACTTTTTATATAGAAATTGCTTTAAAAATATCATATAAATCCATTTTTTAAGTTTATAGTAATTAAAATCCAAATCAAT

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	76.30%	23.60%	0.11%	0.00%	NA
All Indica	2759	98.90%	1.10%	0.04%	0.00%	NA
All Japonica	1512	32.50%	67.30%	0.13%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	97.20%	2.60%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.10%	1.90%	0.00%	0.00%	NA
Temperate Japonica	767	46.30%	53.50%	0.26%	0.00%	NA
Tropical Japonica	504	7.10%	92.90%	0.00%	0.00%	NA
Japonica Intermediate	241	41.90%	58.10%	0.00%	0.00%	NA
VI/Aromatic	96	67.70%	32.30%	0.00%	0.00%	NA
Intermediate	90	58.90%	38.90%	2.22%	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
vg1016644917	G -> A	LOC_Os10g31740.1	upstream_gene_variant ; 4205.0bp to feature; MODIFIER	silent_mutation	Average:44.038; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N
vg1016644917	G -> A	LOC_Os10g31760.1	downstream_gene_variant ; 3899.0bp to feature; MODIFIER	silent_mutation	Average:44.038; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N
vg1016644917	G -> A	LOC_Os10g31750.1	intron_variant ; MODIFIER	silent_mutation	Average:44.038; most accessible tissue: Zhenshan97 root, score: 80.208	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1016644917	NA	2.83E-17	mr1035	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
vg1016644917	7.16E-06	NA	mr1283	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
vg1016644917	NA	4.46E-07	mr1510	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
vg1016644917	NA	3.55E-15	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
vg1016644917	NA	1.27E-09	mr1648	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
vg1016644917	NA	2.14E-06	mr1761	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
vg1016644917	NA	5.30E-13	mr1905	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
vg1016644917	NA	3.49E-07	mr1030_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
vg1016644917	NA	1.16E-13	mr1035_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
vg1016644917	NA	6.80E-19	mr1062_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
vg1016644917	NA	4.47E-12	mr1553_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
vg1016644917	NA	8.03E-08	mr1765_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
vg1016644917	NA	3.77E-18	mr1945_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