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Detailed information for vg0325688031:

Variant ID: vg0325688031 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 25688031
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACTACTTTAAGATCTTTAACCATAGCAAACACTGTTTTCCCGCTGCGATGTTTAGGCTTCGTACGGTGGTCCGCCTTATATTCAAAGTGCTTGCCTTTC[A/T]
TCCGTACCGGGTGGTTTGCTGCAAGGAATCGACGATGACCCATGTACACAACCTTCCTAGAGTGCTTAAGATACATACTTTCTGTTTCATCCATACAGTG

Reverse complement sequence

CACTGTATGGATGAAACAGAAAGTATGTATCTTAAGCACTCTAGGAAGGTTGTGTACATGGGTCATCGTCGATTCCTTGCAGCAAACCACCCGGTACGGA[T/A]
GAAAGGCAAGCACTTTGAATATAAGGCGGACCACCGTACGAAGCCTAAACATCGCAGCGGGAAAACAGTGTTTGCTATGGTTAAAGATCTTAAAGTAGTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.40%	13.30%	4.30%	0.00%	NA
All Indica	2759	97.30%	0.90%	1.81%	0.00%	NA
All Japonica	1512	59.80%	33.60%	6.61%	0.00%	NA
Aus	269	75.80%	23.80%	0.37%	0.00%	NA
Indica I	595	98.50%	0.00%	1.51%	0.00%	NA
Indica II	465	98.50%	0.40%	1.08%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	93.10%	2.40%	4.45%	0.00%	NA
Temperate Japonica	767	53.70%	34.60%	11.73%	0.00%	NA
Tropical Japonica	504	74.60%	24.20%	1.19%	0.00%	NA
Japonica Intermediate	241	48.10%	50.20%	1.66%	0.00%	NA
VI/Aromatic	96	29.20%	22.90%	47.92%	0.00%	NA
Intermediate	90	81.10%	12.20%	6.67%	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
vg0325688031	A -> T	LOC_Os03g45519.1	missense_variant ; p.Met633Lys; MODERATE	nonsynonymous_codon ; M633K	Average:43.745; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	probably damaging	-2.95	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0325688031	2.55E-06	NA	mr1166	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
vg0325688031	4.58E-07	NA	mr1210	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
vg0325688031	5.15E-06	3.90E-06	mr1210	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
vg0325688031	5.91E-08	NA	mr1305	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
vg0325688031	3.08E-06	1.59E-06	mr1305	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
vg0325688031	8.59E-07	NA	mr1585	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
vg0325688031	7.46E-06	NA	mr1585	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
vg0325688031	3.87E-09	NA	mr1586	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
vg0325688031	1.56E-06	1.83E-06	mr1586	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
vg0325688031	4.48E-07	NA	mr1765	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
vg0325688031	NA	9.43E-06	mr1765	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
vg0325688031	8.11E-07	NA	mr1305_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
vg0325688031	4.14E-06	NA	mr1305_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
vg0325688031	1.42E-06	NA	mr1585_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
vg0325688031	9.70E-07	NA	mr1585_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