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Detailed information for vg1122375122:

Variant ID: vg1122375122 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22375122
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTTATATAAGTTATATTGTAGTTACAGTACAGTTAAAATGTAATTACACTTCAATTATACTATAGTTACATATGAAAGTATTTACTCAAAATACTTGC[G/A]
GCAGTTTTTTATATACTCCCATTCCAAACGAAGAAGAGGCATACGTAGTGGAGAATGTTCGATGTTCGTTATATGCCGATGGTGTAGCCCTTTTTGTAAA

Reverse complement sequence

TTTACAAAAAGGGCTACACCATCGGCATATAACGAACATCGAACATTCTCCACTACGTATGCCTCTTCTTCGTTTGGAATGGGAGTATATAAAAAACTGC[C/T]
GCAAGTATTTTGAGTAAATACTTTCATATGTAACTATAGTATAATTGAAGTGTAATTACATTTTAACTGTACTGTAACTACAATATAACTTATATAAAAC

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	38.90%	12.70%	0.21%	48.26%	NA
All Indica	2759	19.30%	17.90%	0.33%	62.49%	NA
All Japonica	1512	74.90%	3.00%	0.00%	22.02%	NA
Aus	269	19.00%	16.40%	0.00%	64.68%	NA
Indica I	595	36.30%	11.80%	0.34%	51.60%	NA
Indica II	465	22.20%	2.20%	0.86%	74.84%	NA
Indica III	913	5.40%	35.60%	0.22%	58.82%	NA
Indica Intermediate	786	21.00%	11.20%	0.13%	67.68%	NA
Temperate Japonica	767	85.80%	3.90%	0.00%	10.30%	NA
Tropical Japonica	504	61.70%	1.60%	0.00%	36.71%	NA
Japonica Intermediate	241	68.00%	3.30%	0.00%	28.63%	NA
VI/Aromatic	96	79.20%	7.30%	0.00%	13.54%	NA
Intermediate	90	48.90%	8.90%	1.11%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122375122	G -> A	LOC_Os11g37780.1	downstream_gene_variant ; 4430.0bp to feature; MODIFIER	silent_mutation	Average:10.434; most accessible tissue: Callus, score: 47.492	N	N	N	N
vg1122375122	G -> A	LOC_Os11g37780-LOC_Os11g37790	intergenic_region ; MODIFIER	silent_mutation	Average:10.434; most accessible tissue: Callus, score: 47.492	N	N	N	N
vg1122375122	G -> DEL	N	N	silent_mutation	Average:10.434; most accessible tissue: Callus, score: 47.492	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122375122	6.26E-07	2.52E-08	mr1517	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
vg1122375122	3.09E-06	3.74E-08	mr1538	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
vg1122375122	NA	7.81E-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