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Detailed information for vg0328202089:

Variant ID: vg0328202089 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 28202089
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAGTACCTGTGGGGGGCACAACAGAAGGCCTAGCCGAGGAAGGCGGGGTGCTGAACGGTGCACGAAACCCTGAAGCAATCGGCAAGTGAAACGGCTCAC[A/T]
TATATGTGCGAGGCATGTGCAGAAAAATCCTTAAAAATACTTACCTCCGTGCGGAGGGGGAGTCGGCCTAGGAACGTGCGCAGCTGGACGGGGACCAGTC

Reverse complement sequence

GACTGGTCCCCGTCCAGCTGCGCACGTTCCTAGGCCGACTCCCCCTCCGCACGGAGGTAAGTATTTTTAAGGATTTTTCTGCACATGCCTCGCACATATA[T/A]
GTGAGCCGTTTCACTTGCCGATTGCTTCAGGGTTTCGTGCACCGTTCAGCACCCCGCCTTCCTCGGCTAGGCCTTCTGTTGTGCCCCCCACAGGTACTTA

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	86.60%	6.00%	7.34%	0.00%	NA
All Indica	2759	86.80%	3.30%	9.89%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	13.80%	61.00%	25.28%	0.00%	NA
Indica I	595	58.00%	5.70%	36.30%	0.00%	NA
Indica II	465	92.50%	3.40%	4.09%	0.00%	NA
Indica III	913	97.00%	2.50%	0.44%	0.00%	NA
Indica Intermediate	786	93.50%	2.20%	4.33%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	79.20%	19.80%	1.04%	0.00%	NA
Intermediate	90	84.40%	11.10%	4.44%	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
vg0328202089	A -> T	LOC_Os03g49530.1	intron_variant ; MODIFIER	silent_mutation	Average:17.617; most accessible tissue: Minghui63 root, score: 29.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0328202089	NA	2.33E-06	mr1006	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
vg0328202089	NA	1.71E-08	mr1038	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
vg0328202089	NA	5.02E-07	mr1038	Ind_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
vg0328202089	NA	4.53E-06	mr1052	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
vg0328202089	NA	6.22E-10	mr1389	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
vg0328202089	NA	1.10E-07	mr1389	Ind_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
vg0328202089	NA	9.03E-06	mr1433	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
vg0328202089	NA	3.09E-06	mr1621	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
vg0328202089	1.64E-06	1.63E-06	mr1753	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
vg0328202089	NA	5.59E-07	mr1764	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
vg0328202089	NA	3.43E-07	mr1810	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
vg0328202089	NA	1.80E-06	mr1931	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
vg0328202089	NA	9.05E-06	mr1948	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
vg0328202089	NA	1.61E-06	mr1038_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
vg0328202089	NA	2.21E-06	mr1389_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
vg0328202089	NA	3.70E-06	mr1389_2	Ind_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