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Detailed information for vg0622417280:

Variant ID: vg0622417280 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22417280
Reference Allele: T	Alternative Allele: C,G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGTTGCTCCTCAAAGTATGGGTCAACTTCTGCCATATGTTGGAGCACAACGTAATGAGCCTGCGCGTAGGAAGCTTGATCGGGCCTAATTCTTTTTCT[T/C,G]
CCGATTGTGCCAACACCTGACAACCTTCCTTCGTGACGAGACGCTGGAACTCCGATAGGATCGACATCGGACATGTAATTGACGCAGAACTCGATAGCCT

Reverse complement sequence

AGGCTATCGAGTTCTGCGTCAATTACATGTCCGATGTCGATCCTATCGGAGTTCCAGCGTCTCGTCACGAAGGAAGGTTGTCAGGTGTTGGCACAATCGG[A/G,C]
AGAAAAAGAATTAGGCCCGATCAAGCTTCCTACGCGCAGGCTCATTACGTTGTGCTCCAACATATGGCAGAAGTTGACCCATACTTTGAGGAGCAACACT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.30%	2.20%	0.51%	4.36%	C: 0.63%
All Indica	2759	97.60%	0.00%	0.14%	2.17%	NA
All Japonica	1512	80.80%	6.70%	1.32%	9.33%	C: 1.92%
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	96.30%	0.00%	0.43%	3.23%	NA
Indica III	913	96.50%	0.00%	0.00%	3.50%	NA
Indica Intermediate	786	98.00%	0.10%	0.25%	1.65%	NA
Temperate Japonica	767	97.30%	1.60%	0.52%	0.65%	NA
Tropical Japonica	504	56.70%	14.90%	2.98%	20.04%	C: 5.36%
Japonica Intermediate	241	78.40%	5.80%	0.41%	14.52%	C: 0.83%
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	1.10%	0.00%	5.56%	C: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622417280	T -> C	LOC_Os06g37860.1	synonymous_variant ; p.Gly461Gly; LOW	synonymous_codon	Average:45.247; most accessible tissue: Zhenshan97 young leaf, score: 67.334	N	N	N	N
vg0622417280	T -> G	LOC_Os06g37860.1	synonymous_variant ; p.Gly461Gly; LOW	synonymous_codon	Average:45.247; most accessible tissue: Zhenshan97 young leaf, score: 67.334	N	N	N	N
vg0622417280	T -> DEL	LOC_Os06g37860.1	N	frameshift_variant	Average:45.247; most accessible tissue: Zhenshan97 young leaf, score: 67.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622417280	NA	5.06E-06	mr1040	Jap_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
vg0622417280	NA	1.37E-08	mr1248	Jap_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
vg0622417280	2.25E-06	2.25E-06	mr1254	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
vg0622417280	NA	1.24E-06	mr1668	Jap_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
vg0622417280	NA	2.29E-07	mr1951	Jap_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
vg0622417280	NA	3.72E-09	mr1676_2	Jap_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