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Detailed information for vg0519909748:

Variant ID: vg0519909748 (JBrowse)	Variation Type: INDEL
Chromosome: chr05	Position: 19909748
Reference Allele: TGC	Alternative Allele: T
Primary Allele: TGC	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTACCACCTTGCTTATTCTAGGAGAGGGGGACCTCCTTAAAAGGGAGGATGCCCTCCTAGCCACTTGAAGCATGTGTGGTGGAGAGAAGAGGGGAAACA[TGC/T]
GCGCGCTCGCTCGCCTCGCCGGGCCGGGCCGGCAACGCGCGTGCACGACGTACGCGTCGAATGGTCCGAAAAATTGGCTCCTCACCCTTGCGCAGATGCA

Reverse complement sequence

TGCATCTGCGCAAGGGTGAGGAGCCAATTTTTCGGACCATTCGACGCGTACGTCGTGCACGCGCGTTGCCGGCCCGGCCCGGCGAGGCGAGCGAGCGCGC[GCA/A]
TGTTTCCCCTCTTCTCTCCACCACACATGCTTCAAGTGGCTAGGAGGGCATCCTCCCTTTTAAGGAGGTCCCCCTCTCCTAGAATAAGCAAGGTGGTACT

Allele Frequencies:

Populations	Population Size	Frequency of TGC(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	29.40%	0.30%	1.71%	68.54%	NA
All Indica	2759	4.20%	0.50%	1.56%	93.66%	NA
All Japonica	1512	62.90%	0.00%	0.33%	36.77%	NA
Aus	269	74.70%	0.00%	11.90%	13.38%	NA
Indica I	595	0.70%	0.00%	0.50%	98.82%	NA
Indica II	465	1.30%	0.00%	0.86%	97.85%	NA
Indica III	913	6.50%	1.50%	2.52%	89.49%	NA
Indica Intermediate	786	6.10%	0.10%	1.65%	92.11%	NA
Temperate Japonica	767	94.70%	0.00%	0.00%	5.35%	NA
Tropical Japonica	504	7.10%	0.00%	0.60%	92.26%	NA
Japonica Intermediate	241	78.40%	0.00%	0.83%	20.75%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	31.10%	0.00%	1.11%	67.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0519909748	TGC -> T	LOC_Os05g33790.1	upstream_gene_variant ; 795.0bp to feature; MODIFIER	silent_mutation	Average:25.026; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N
vg0519909748	TGC -> T	LOC_Os05g33780-LOC_Os05g33790	intergenic_region ; MODIFIER	silent_mutation	Average:25.026; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N
vg0519909748	TGC -> DEL	N	N	silent_mutation	Average:25.026; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0519909748	NA	2.33E-07	mr1157	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
vg0519909748	NA	2.25E-18	mr1179	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
vg0519909748	NA	1.97E-06	mr1231	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
vg0519909748	NA	3.49E-22	mr1422	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
vg0519909748	NA	9.59E-09	mr1446	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
vg0519909748	2.41E-06	2.41E-06	mr1717	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
vg0519909748	7.20E-07	7.20E-07	mr1770	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
vg0519909748	NA	2.67E-15	mr1807	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
vg0519909748	NA	1.47E-08	mr1989	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
vg0519909748	NA	2.42E-07	mr1446_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
vg0519909748	NA	6.00E-17	mr1457_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
vg0519909748	NA	6.34E-15	mr1720_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
vg0519909748	NA	2.16E-15	mr1807_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