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Detailed information for vg1122373560:

Variant ID: vg1122373560 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22373560
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTTGAACACACCAAACAAGAGAAGAGAGGACCCAAACTGAAAAAAGCAAAACAAAATGTGGAGCTAGAAGGCCTCGTCAAAGCCTAGGATTGAAGTTC[G/A]
AAGCCAATGCAAAGACCAATGACAATATCCTTGCACGAAGAGATTTCTCCAAAGCGGTGCCCTCAAGGAGGATGTGACGTGGATCGCCGCCACCGCTCGT

Reverse complement sequence

ACGAGCGGTGGCGGCGATCCACGTCACATCCTCCTTGAGGGCACCGCTTTGGAGAAATCTCTTCGTGCAAGGATATTGTCATTGGTCTTTGCATTGGCTT[C/T]
GAACTTCAATCCTAGGCTTTGACGAGGCCTTCTAGCTCCACATTTTGTTTTGCTTTTTTCAGTTTGGGTCCTCTCTTCTCTTGTTTGGTGTGTTCAACTT

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	41.70%	0.30%	1.23%	56.83%	NA
All Indica	2759	22.80%	0.10%	1.92%	75.21%	NA
All Japonica	1512	77.20%	0.10%	0.00%	22.75%	NA
Aus	269	19.30%	1.50%	1.12%	78.07%	NA
Indica I	595	43.20%	0.20%	0.67%	55.97%	NA
Indica II	465	24.90%	0.20%	2.15%	72.69%	NA
Indica III	913	6.90%	0.00%	2.85%	90.25%	NA
Indica Intermediate	786	24.40%	0.10%	1.65%	73.79%	NA
Temperate Japonica	767	85.70%	0.00%	0.00%	14.34%	NA
Tropical Japonica	504	68.50%	0.00%	0.00%	31.55%	NA
Japonica Intermediate	241	68.50%	0.40%	0.00%	31.12%	NA
VI/Aromatic	96	75.00%	5.20%	0.00%	19.79%	NA
Intermediate	90	55.60%	0.00%	2.22%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122373560	G -> A	LOC_Os11g37780.1	downstream_gene_variant ; 2868.0bp to feature; MODIFIER	silent_mutation	Average:11.097; most accessible tissue: Callus, score: 41.06	N	N	N	N
vg1122373560	G -> A	LOC_Os11g37780-LOC_Os11g37790	intergenic_region ; MODIFIER	silent_mutation	Average:11.097; most accessible tissue: Callus, score: 41.06	N	N	N	N
vg1122373560	G -> DEL	N	N	silent_mutation	Average:11.097; most accessible tissue: Callus, score: 41.06	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122373560	2.80E-07	4.09E-09	mr1517	Jap_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
vg1122373560	3.28E-06	1.54E-08	mr1538	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
vg1122373560	NA	1.32E-06	mr1517_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
vg1122373560	NA	1.09E-08	mr1538_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