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Detailed information for vg0720910687:

Variant ID: vg0720910687 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 20910687
Reference Allele: A	Alternative Allele: G,C
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTGAAACAAGATTAAAACATATTGCATTGTAATATGGAGAACCAGTTGCTCTTGATACAAATCGAACAGGAGAACATTAACAATATTAAAAAACTATA[A/G,C]
AAACAAAAATTTGATAGATGAAGGTCAGAAATGGTATGAATGACTACATACCTACCAGTCTTATAAATCCAACCTGAATACAAAATGGCTGTATTTTACA

Reverse complement sequence

TGTAAAATACAGCCATTTTGTATTCAGGTTGGATTTATAAGACTGGTAGGTATGTAGTCATTCATACCATTTCTGACCTTCATCTATCAAATTTTTGTTT[T/C,G]
TATAGTTTTTTAATATTGTTAATGTTCTCCTGTTCGATTTGTATCAAGAGCAACTGGTTCTCCATATTACAATGCAATATGTTTTAATCTTGTTTCACAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.80%	14.90%	7.64%	31.78%	C: 0.87%
All Indica	2759	26.70%	8.60%	10.44%	52.85%	C: 1.45%
All Japonica	1512	84.40%	15.10%	0.26%	0.20%	NA
Aus	269	2.60%	76.20%	13.75%	7.43%	NA
Indica I	595	20.50%	1.00%	4.03%	74.45%	NA
Indica II	465	19.80%	4.10%	10.11%	65.38%	C: 0.65%
Indica III	913	28.30%	16.80%	18.07%	33.52%	C: 3.40%
Indica Intermediate	786	33.70%	7.40%	6.62%	51.53%	C: 0.76%
Temperate Japonica	767	82.70%	16.70%	0.26%	0.39%	NA
Tropical Japonica	504	83.10%	16.70%	0.20%	0.00%	NA
Japonica Intermediate	241	92.50%	7.10%	0.41%	0.00%	NA
VI/Aromatic	96	44.80%	24.00%	30.21%	0.00%	C: 1.04%
Intermediate	90	61.10%	12.20%	3.33%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0720910687	A -> DEL	N	N	silent_mutation	Average:11.288; most accessible tissue: Callus, score: 67.906	N	N	N	N
vg0720910687	A -> G	LOC_Os07g34890.1	upstream_gene_variant ; 1521.0bp to feature; MODIFIER	silent_mutation	Average:11.288; most accessible tissue: Callus, score: 67.906	N	N	N	N
vg0720910687	A -> G	LOC_Os07g34880.1	downstream_gene_variant ; 4855.0bp to feature; MODIFIER	silent_mutation	Average:11.288; most accessible tissue: Callus, score: 67.906	N	N	N	N
vg0720910687	A -> G	LOC_Os07g34880-LOC_Os07g34890	intergenic_region ; MODIFIER	silent_mutation	Average:11.288; most accessible tissue: Callus, score: 67.906	N	N	N	N
vg0720910687	A -> C	LOC_Os07g34890.1	upstream_gene_variant ; 1521.0bp to feature; MODIFIER	silent_mutation	Average:11.288; most accessible tissue: Callus, score: 67.906	N	N	N	N
vg0720910687	A -> C	LOC_Os07g34880.1	downstream_gene_variant ; 4855.0bp to feature; MODIFIER	silent_mutation	Average:11.288; most accessible tissue: Callus, score: 67.906	N	N	N	N
vg0720910687	A -> C	LOC_Os07g34880-LOC_Os07g34890	intergenic_region ; MODIFIER	silent_mutation	Average:11.288; most accessible tissue: Callus, score: 67.906	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720910687	NA	3.30E-07	mr1057_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
vg0720910687	1.62E-06	NA	mr1807_2	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