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Detailed information for vg0419784082:

Variant ID: vg0419784082 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 19784082
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGCTTAATAAATTCGTCTCGCGGTTTACTGACGGATTCTGTAATTAGTTTTTTTATTAGTATCCGAACACCCTATGCGACACTCTATATATATATACCA[C/T]
ATGTAACACGCCAAAACTTTACACCCTTGGATCTAAACACCCCAGCACCCCATGGCAGCACAGTTATCATCTGACTGATCATTATCTGCAGGTTGACCAT

Reverse complement sequence

ATGGTCAACCTGCAGATAATGATCAGTCAGATGATAACTGTGCTGCCATGGGGTGCTGGGGTGTTTAGATCCAAGGGTGTAAAGTTTTGGCGTGTTACAT[G/A]
TGGTATATATATATAGAGTGTCGCATAGGGTGTTCGGATACTAATAAAAAAACTAATTACAGAATCCGTCAGTAAACCGCGAGACGAATTTATTAAGCCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.10%	36.40%	0.49%	0.00%	NA
All Indica	2759	94.10%	5.70%	0.22%	0.00%	NA
All Japonica	1512	14.90%	84.30%	0.73%	0.00%	NA
Aus	269	40.50%	58.40%	1.12%	0.00%	NA
Indica I	595	93.30%	6.40%	0.34%	0.00%	NA
Indica II	465	94.40%	4.70%	0.86%	0.00%	NA
Indica III	913	95.70%	4.30%	0.00%	0.00%	NA
Indica Intermediate	786	92.70%	7.30%	0.00%	0.00%	NA
Temperate Japonica	767	22.20%	76.80%	1.04%	0.00%	NA
Tropical Japonica	504	2.20%	97.60%	0.20%	0.00%	NA
Japonica Intermediate	241	18.70%	80.50%	0.83%	0.00%	NA
VI/Aromatic	96	22.90%	77.10%	0.00%	0.00%	NA
Intermediate	90	30.00%	66.70%	3.33%	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
vg0419784082	C -> T	LOC_Os04g32780-LOC_Os04g32790	intergenic_region ; MODIFIER	silent_mutation	Average:56.492; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0419784082	NA	1.10E-08	mr1047	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
vg0419784082	NA	7.35E-10	mr1151	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
vg0419784082	NA	5.08E-18	mr1164	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
vg0419784082	NA	3.09E-08	mr1174	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
vg0419784082	NA	1.12E-14	mr1261	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
vg0419784082	NA	7.75E-06	mr1450	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
vg0419784082	NA	1.91E-20	mr1580	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
vg0419784082	NA	2.53E-20	mr1627	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
vg0419784082	NA	1.80E-06	mr1627	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
vg0419784082	NA	6.10E-20	mr1825	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
vg0419784082	NA	9.38E-07	mr1321_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
vg0419784082	NA	1.55E-12	mr1514_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