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Detailed information for vg0222636576:

Variant ID: vg0222636576 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22636576
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTATCATTTAGTTTATTATGACTTGATTCGTCATCAAATGTTCTTTAAGCATGACATAAATATTTTCATATTTGCATAAAAGTTTTGAATAAAACGAAT[G/A]
GTCAAACGTTAGTTGAAAAGTCAACGGCGTTGTACATTAGGATACGGAGGGAGTACGATATTTATGCATCCACGCATGCATGCAGAGGCGGCCAACTCGC

Reverse complement sequence

GCGAGTTGGCCGCCTCTGCATGCATGCGTGGATGCATAAATATCGTACTCCCTCCGTATCCTAATGTACAACGCCGTTGACTTTTCAACTAACGTTTGAC[C/T]
ATTCGTTTTATTCAAAACTTTTATGCAAATATGAAAATATTTATGTCATGCTTAAAGAACATTTGATGACGAATCAAGTCATAATAAACTAAATGATAAT

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	79.60%	20.40%	0.08%	0.00%	NA
All Indica	2759	96.30%	3.70%	0.04%	0.00%	NA
All Japonica	1512	57.70%	42.20%	0.13%	0.00%	NA
Aus	269	32.70%	67.30%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	93.30%	6.50%	0.22%	0.00%	NA
Indica III	913	98.00%	2.00%	0.00%	0.00%	NA
Indica Intermediate	786	94.00%	6.00%	0.00%	0.00%	NA
Temperate Japonica	767	81.20%	18.80%	0.00%	0.00%	NA
Tropical Japonica	504	25.80%	73.80%	0.40%	0.00%	NA
Japonica Intermediate	241	49.40%	50.60%	0.00%	0.00%	NA
VI/Aromatic	96	80.20%	19.80%	0.00%	0.00%	NA
Intermediate	90	73.30%	25.60%	1.11%	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
vg0222636576	G -> A	LOC_Os02g37510.1	downstream_gene_variant ; 1706.0bp to feature; MODIFIER	silent_mutation	Average:55.54; most accessible tissue: Minghui63 root, score: 75.485	N	N	N	N
vg0222636576	G -> A	LOC_Os02g37500.1	intron_variant ; MODIFIER	silent_mutation	Average:55.54; most accessible tissue: Minghui63 root, score: 75.485	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222636576	4.65E-06	NA	mr1117	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
vg0222636576	9.93E-06	NA	mr1118	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
vg0222636576	NA	5.26E-06	mr1518	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
vg0222636576	5.37E-06	NA	mr1113_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
vg0222636576	2.09E-06	NA	mr1114_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
vg0222636576	7.33E-08	NA	mr1117_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
vg0222636576	2.21E-07	NA	mr1118_2	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
vg0222636576	2.04E-07	NA	mr1119_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
vg0222636576	9.97E-06	NA	mr1120_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
vg0222636576	8.96E-07	NA	mr1123_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
vg0222636576	3.18E-06	NA	mr1240_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
vg0222636576	9.17E-08	NA	mr1242_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
vg0222636576	5.46E-09	NA	mr1496_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