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Detailed information for vg0319057447:

Variant ID: vg0319057447 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 19057447
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGCGTAACCTGCGTCATCACTCCGGCCATTATGCAAGAAGAAGACAAGTCACTCGCCTTGTGGTCACTGGAGCAAACGCCATACCTGTGAGGCCTCGTG[C/T]
TAATCATAACCCATAGCAGAAACAATGTACCGATGCTAAGCACCTTTCCTTTTTTTTAGGCAGTGCTTAGTATTCATGTAATAAGGGAGAAATGTATAAT

Reverse complement sequence

ATTATACATTTCTCCCTTATTACATGAATACTAAGCACTGCCTAAAAAAAAGGAAAGGTGCTTAGCATCGGTACATTGTTTCTGCTATGGGTTATGATTA[G/A]
CACGAGGCCTCACAGGTATGGCGTTTGCTCCAGTGACCACAAGGCGAGTGACTTGTCTTCTTCTTGCATAATGGCCGGAGTGATGACGCAGGTTACGCTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.70%	32.50%	0.47%	6.33%	NA
All Indica	2759	91.10%	3.20%	0.36%	5.40%	NA
All Japonica	1512	3.00%	86.70%	0.66%	9.66%	NA
Aus	269	90.00%	10.00%	0.00%	0.00%	NA
Indica I	595	97.50%	2.00%	0.17%	0.34%	NA
Indica II	465	95.70%	3.20%	0.00%	1.08%	NA
Indica III	913	84.00%	1.60%	0.77%	13.58%	NA
Indica Intermediate	786	91.70%	5.70%	0.25%	2.29%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	7.50%	66.30%	0.79%	25.40%	NA
Japonica Intermediate	241	2.10%	88.00%	2.49%	7.47%	NA
VI/Aromatic	96	26.00%	71.90%	0.00%	2.08%	NA
Intermediate	90	46.70%	48.90%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0319057447	C -> T	LOC_Os03g33328.1	upstream_gene_variant ; 2274.0bp to feature; MODIFIER	silent_mutation	Average:43.237; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg0319057447	C -> T	LOC_Os03g33310.1	downstream_gene_variant ; 4359.0bp to feature; MODIFIER	silent_mutation	Average:43.237; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg0319057447	C -> T	LOC_Os03g33319.1	intron_variant ; MODIFIER	silent_mutation	Average:43.237; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg0319057447	C -> DEL	N	N	silent_mutation	Average:43.237; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0319057447	NA	3.97E-07	mr1136	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
vg0319057447	NA	5.03E-11	mr1188	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
vg0319057447	5.27E-07	1.10E-07	mr1188	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
vg0319057447	NA	3.85E-11	mr1281	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
vg0319057447	NA	2.43E-07	mr1448	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
vg0319057447	NA	1.49E-21	mr1588	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
vg0319057447	NA	4.78E-11	mr1630	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
vg0319057447	NA	6.16E-115	mr1750	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
vg0319057447	NA	4.36E-16	mr1842	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
vg0319057447	NA	3.88E-12	mr1188_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
vg0319057447	NA	1.29E-07	mr1188_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
vg0319057447	NA	4.35E-06	mr1217_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
vg0319057447	NA	2.43E-24	mr1588_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
vg0319057447	8.22E-06	1.39E-151	mr1750_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
vg0319057447	NA	1.26E-12	mr1770_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