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Detailed information for vg0804944075:

Variant ID: vg0804944075 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4944075
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGGATTAGAGAAGTCCTACTTGGAAAGGGTAAAATCTCTAGTATATCGTGTCGGTTTACATATCTCCAAGTCTTACTTGAGGGTCAAGGTATCCCACG[A/G]
TATAAAAGGGACCCCTAGGGAGAGGCGAAGGGCATCGCACCTCATCGCCAACACACCCACCAAAGTTTACGAAGCCGGAGTCCACGGAGCCAACTCGCCG

Reverse complement sequence

CGGCGAGTTGGCTCCGTGGACTCCGGCTTCGTAAACTTTGGTGGGTGTGTTGGCGATGAGGTGCGATGCCCTTCGCCTCTCCCTAGGGGTCCCTTTTATA[T/C]
CGTGGGATACCTTGACCCTCAAGTAAGACTTGGAGATATGTAAACCGACACGATATACTAGAGATTTTACCCTTTCCAAGTAGGACTTCTCTAATCCCTT

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	66.70%	6.70%	2.14%	24.44%	NA
All Indica	2759	64.80%	8.20%	2.36%	24.61%	NA
All Japonica	1512	73.80%	0.60%	0.40%	25.20%	NA
Aus	269	53.50%	27.90%	7.06%	11.52%	NA
Indica I	595	96.80%	0.20%	0.00%	3.03%	NA
Indica II	465	43.70%	8.40%	3.87%	44.09%	NA
Indica III	913	52.80%	13.40%	3.40%	30.45%	NA
Indica Intermediate	786	67.20%	8.10%	2.04%	22.65%	NA
Temperate Japonica	767	95.40%	0.00%	0.13%	4.43%	NA
Tropical Japonica	504	38.90%	1.80%	0.60%	58.73%	NA
Japonica Intermediate	241	78.00%	0.00%	0.83%	21.16%	NA
VI/Aromatic	96	45.80%	5.20%	8.33%	40.62%	NA
Intermediate	90	66.70%	2.20%	3.33%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804944075	A -> G	LOC_Os08g08560.1	upstream_gene_variant ; 638.0bp to feature; MODIFIER	silent_mutation	Average:27.661; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0804944075	A -> G	LOC_Os08g08570.1	upstream_gene_variant ; 3163.0bp to feature; MODIFIER	silent_mutation	Average:27.661; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0804944075	A -> G	LOC_Os08g08560-LOC_Os08g08570	intergenic_region ; MODIFIER	silent_mutation	Average:27.661; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0804944075	A -> DEL	N	N	silent_mutation	Average:27.661; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804944075	2.15E-06	NA	mr1188	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
vg0804944075	NA	8.51E-08	mr1642_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