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Detailed information for vg0202888284:

Variant ID: vg0202888284 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2888284
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGCTAATGAACTTGCCACCCGCGTCGGTCCACTCTTGGGAGGATTTGTGCCAGCAGTTCACCACGAACTTCCAGGGCACATATCTGTGCCCAGGCGAA[G/A]
AAGCGGACTTGCATGCGGTACAGCGAAGGGACGATGAGTCTCTTCGCTTGTACATTCAGCGGTTCTGTCAAGTCCGCAACACCATACCGTGCATCCCCGC

Reverse complement sequence

GCGGGGATGCACGGTATGGTGTTGCGGACTTGACAGAACCGCTGAATGTACAAGCGAAGAGACTCATCGTCCCTTCGCTGTACCGCATGCAAGTCCGCTT[C/T]
TTCGCCTGGGCACAGATATGTGCCCTGGAAGTTCGTGGTGAACTGCTGGCACAAATCCTCCCAAGAGTGGACCGACGCGGGTGGCAAGTTCATTAGCCAA

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	50.40%	11.40%	10.66%	27.51%	NA
All Indica	2759	55.70%	0.40%	14.17%	29.65%	NA
All Japonica	1512	48.50%	33.70%	0.86%	16.93%	NA
Aus	269	16.40%	0.70%	14.50%	68.40%	NA
Indica I	595	70.30%	0.20%	4.20%	25.38%	NA
Indica II	465	67.10%	0.90%	7.74%	24.30%	NA
Indica III	913	39.30%	0.70%	23.99%	36.04%	NA
Indica Intermediate	786	57.10%	0.10%	14.12%	28.63%	NA
Temperate Japonica	767	66.80%	8.60%	1.17%	23.47%	NA
Tropical Japonica	504	13.70%	78.20%	0.60%	7.54%	NA
Japonica Intermediate	241	63.50%	20.30%	0.41%	15.77%	NA
VI/Aromatic	96	16.70%	1.00%	51.04%	31.25%	NA
Intermediate	90	54.40%	18.90%	13.33%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0202888284	G -> A	LOC_Os02g05850.1	missense_variant ; p.Glu251Lys; MODERATE	nonsynonymous_codon ; E251K	Average:41.015; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	benign	0.917	DELETERIOUS	0.02
vg0202888284	G -> DEL	LOC_Os02g05850.1	N	frameshift_variant	Average:41.015; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202888284	NA	6.60E-08	mr1668	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
vg0202888284	NA	1.96E-07	mr1308_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
vg0202888284	NA	1.51E-10	mr1379_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
vg0202888284	NA	2.92E-06	mr1379_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
vg0202888284	NA	6.91E-08	mr1401_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
vg0202888284	NA	3.06E-08	mr1408_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
vg0202888284	NA	2.51E-08	mr1449_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
vg0202888284	NA	2.08E-10	mr1584_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
vg0202888284	NA	8.25E-08	mr1606_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
vg0202888284	NA	3.30E-08	mr1819_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
vg0202888284	NA	4.85E-06	mr1852_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
vg0202888284	NA	4.15E-06	mr1873_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
vg0202888284	NA	5.29E-10	mr1905_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
vg0202888284	3.11E-06	3.11E-06	mr1930_2	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