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Detailed information for vg0410781389:

Variant ID: vg0410781389 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10781389
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAGCGTCCTATCTTGCCGCGCGCTGCGCCGCAGCGCGTAGGCCTCGAGATCGCTTGTGCGTGCCCGACTGCCTTCGCGCGCCATCGCCCGTCCGACGCC[C/A]
TCAGACCGCCGCCGCCGCACCAATCTTGACGACGACAAAGCCAGGACGACCTCTGCCGCAAGAAATCACAGCTCGACGCCGTGCGCTCCCGTCCAACGCT

Reverse complement sequence

AGCGTTGGACGGGAGCGCACGGCGTCGAGCTGTGATTTCTTGCGGCAGAGGTCGTCCTGGCTTTGTCGTCGTCAAGATTGGTGCGGCGGCGGCGGTCTGA[G/T]
GGCGTCGGACGGGCGATGGCGCGCGAAGGCAGTCGGGCACGCACAAGCGATCTCGAGGCCTACGCGCTGCGGCGCAGCGCGCGGCAAGATAGGACGCTAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.50%	3.10%	0.34%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	89.30%	9.70%	1.06%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	93.00%	5.70%	1.30%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	57.30%	40.20%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	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
vg0410781389	C -> A	LOC_Os04g19360.1	upstream_gene_variant ; 4104.0bp to feature; MODIFIER	silent_mutation	Average:60.813; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N
vg0410781389	C -> A	LOC_Os04g19370.1	upstream_gene_variant ; 911.0bp to feature; MODIFIER	silent_mutation	Average:60.813; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N
vg0410781389	C -> A	LOC_Os04g19360-LOC_Os04g19370	intergenic_region ; MODIFIER	silent_mutation	Average:60.813; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410781389	8.75E-07	5.06E-06	mr1719	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