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Detailed information for vg0905282844:

Variant ID: vg0905282844 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5282844
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGGGGGAGCGTGTGCTCACGTTTCTCGCCAGAGCCTCAAGGCCATGAAGCGAGAGCTTCTGGCCACGGCCCCTACTCATGAGGCGACGCGTCGGGCGCG[G/A]
TGGTCGGAGATTGCCCTCACCTTTGACCAGACCGACCACCCACCGTGTGTTGCCCGGGAAGGACAGATCGCGATGGTGGTTTCCCCCACCGTTTGCAACG

Reverse complement sequence

CGTTGCAAACGGTGGGGGAAACCACCATCGCGATCTGTCCTTCCCGGGCAACACACGGTGGGTGGTCGGTCTGGTCAAAGGTGAGGGCAATCTCCGACCA[C/T]
CGCGCCCGACGCGTCGCCTCATGAGTAGGGGCCGTGGCCAGAAGCTCTCGCTTCATGGCCTTGAGGCTCTGGCGAGAAACGTGAGCACACGCTCCCCCAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.60%	1.00%	10.83%	34.53%	NA
All Indica	2759	34.60%	1.70%	17.40%	46.36%	NA
All Japonica	1512	83.60%	0.00%	0.93%	15.48%	NA
Aus	269	90.30%	0.70%	3.72%	5.20%	NA
Indica I	595	19.30%	1.50%	14.45%	64.71%	NA
Indica II	465	55.90%	1.30%	11.61%	31.18%	NA
Indica III	913	29.80%	1.90%	24.42%	43.92%	NA
Indica Intermediate	786	39.10%	1.80%	14.89%	44.27%	NA
Temperate Japonica	767	90.60%	0.00%	0.39%	9.00%	NA
Tropical Japonica	504	86.30%	0.00%	1.79%	11.90%	NA
Japonica Intermediate	241	55.60%	0.00%	0.83%	43.57%	NA
VI/Aromatic	96	17.70%	0.00%	4.17%	78.12%	NA
Intermediate	90	62.20%	0.00%	4.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0905282844	G -> DEL	LOC_Os09g09760.1	N	frameshift_variant	Average:12.743; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0905282844	G -> A	LOC_Os09g09760.1	synonymous_variant ; p.Arg475Arg; LOW	synonymous_codon	Average:12.743; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905282844	NA	5.97E-06	mr1417_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
vg0905282844	4.54E-06	4.54E-06	mr1417_2	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