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Detailed information for vg0319678890:

Variant ID: vg0319678890 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 19678890
Reference Allele: C	Alternative Allele: T,CAGCT
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGTCTCCTCTCGCCCTTTGGCATTTCTTTGTGAAACGGTTTTGAAAATTCTCCTCCCTGTCCCTCCAATTCTTTTAGTGTCAAACCTGGAGGGCAAAC[C/T,CAGCT]
GTCAGTTTCGTGTCTGTCCAGAAGTCAAGTCGAGTCTCAAGCTTCGTGCAGCAAAGAACGAGAAGGTCAGTTCAGAGTCGTCGTTCCGCGAAGATCAAGA

Reverse complement sequence

TCTTGATCTTCGCGGAACGACGACTCTGAACTGACCTTCTCGTTCTTTGCTGCACGAAGCTTGAGACTCGACTTGACTTCTGGACAGACACGAAACTGAC[G/A,AGCTG]
GTTTGCCCTCCAGGTTTGACACTAAAAGAATTGGAGGGACAGGGAGGAGAATTTTCAAAACCGTTTCACAAAGAAATGCCAAAGGGCGAGAGGAGACATT

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	83.30%	5.90%	9.20%	1.63%	NA
All Indica	2759	78.90%	9.00%	12.07%	0.00%	NA
All Japonica	1512	93.10%	0.10%	1.65%	5.09%	NA
Aus	269	66.90%	7.80%	25.28%	0.00%	NA
Indica I	595	81.50%	4.50%	13.95%	0.00%	NA
Indica II	465	88.00%	6.50%	5.59%	0.00%	NA
Indica III	913	72.80%	12.50%	14.68%	0.00%	NA
Indica Intermediate	786	78.60%	9.90%	11.45%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	81.50%	0.20%	3.97%	14.29%	NA
Japonica Intermediate	241	95.40%	0.40%	2.07%	2.07%	NA
VI/Aromatic	96	93.80%	2.10%	4.17%	0.00%	NA
Intermediate	90	91.10%	3.30%	5.56%	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
vg0319678890	C -> T	LOC_Os03g35490.1	upstream_gene_variant ; 1956.0bp to feature; MODIFIER	silent_mutation	Average:25.269; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0319678890	C -> T	LOC_Os03g35500.1	upstream_gene_variant ; 661.0bp to feature; MODIFIER	silent_mutation	Average:25.269; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0319678890	C -> T	LOC_Os03g35510.1	downstream_gene_variant ; 2924.0bp to feature; MODIFIER	silent_mutation	Average:25.269; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0319678890	C -> T	LOC_Os03g35490-LOC_Os03g35500	intergenic_region ; MODIFIER	silent_mutation	Average:25.269; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0319678890	C -> DEL	N	N	silent_mutation	Average:25.269; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0319678890	C -> CAGCT	LOC_Os03g35490.1	upstream_gene_variant ; 1957.0bp to feature; MODIFIER	N	Average:25.269; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0319678890	C -> CAGCT	LOC_Os03g35500.1	upstream_gene_variant ; 660.0bp to feature; MODIFIER	N	Average:25.269; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0319678890	C -> CAGCT	LOC_Os03g35510.1	downstream_gene_variant ; 2923.0bp to feature; MODIFIER	N	Average:25.269; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0319678890	C -> CAGCT	LOC_Os03g35490-LOC_Os03g35500	intergenic_region ; MODIFIER	N	Average:25.269; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0319678890	2.85E-06	5.24E-06	mr1668	Ind_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