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Detailed information for vg0610552218:

Variant ID: vg0610552218 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10552218
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

GGGCAAATCTCCACAGAAACAACTTCACCTTATTAGCCACTTTGCAATCCCAGATCTTTTTCCAGTTGAAATTCACCCCTGTGCAGTCTCCCCCACCAGA[T/C]
GAGGATGCTTCTTTGCCACTTCTAGCATCTTTGTTCTGTATCGCCACTTTGTAGGCCGATTTAACTGAAAAAACCCCTTTTTGGTCATAGTGCCAGGCAG

Reverse complement sequence

CTGCCTGGCACTATGACCAAAAAGGGGTTTTTTCAGTTAAATCGGCCTACAAAGTGGCGATACAGAACAAAGATGCTAGAAGTGGCAAAGAAGCATCCTC[A/G]
TCTGGTGGGGGAGACTGCACAGGGGTGAATTTCAACTGGAAAAAGATCTGGGATTGCAAAGTGGCTAATAAGGTGAAGTTGTTTCTGTGGAGATTTGCCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.30%	9.00%	0.21%	15.49%	NA
All Indica	2759	77.30%	0.40%	0.33%	21.93%	NA
All Japonica	1512	66.10%	27.10%	0.07%	6.75%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	98.30%	0.80%	0.17%	0.67%	NA
Indica II	465	91.00%	0.00%	0.00%	9.03%	NA
Indica III	913	61.10%	0.00%	0.33%	38.55%	NA
Indica Intermediate	786	72.30%	0.80%	0.64%	26.34%	NA
Temperate Japonica	767	46.00%	48.80%	0.13%	5.08%	NA
Tropical Japonica	504	90.70%	0.00%	0.00%	9.33%	NA
Japonica Intermediate	241	78.80%	14.50%	0.00%	6.64%	NA
VI/Aromatic	96	89.60%	0.00%	0.00%	10.42%	NA
Intermediate	90	77.80%	7.80%	0.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610552218	T -> C	LOC_Os06g18130.1	synonymous_variant ; p.Ser75Ser; LOW	synonymous_codon	Average:72.675; most accessible tissue: Zhenshan97 flower, score: 86.194	N	N	N	N
vg0610552218	T -> DEL	LOC_Os06g18130.1	N	frameshift_variant	Average:72.675; most accessible tissue: Zhenshan97 flower, score: 86.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610552218	8.72E-10	NA	mr1087	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
vg0610552218	4.22E-08	1.33E-11	mr1087	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
vg0610552218	NA	4.84E-07	mr1096	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
vg0610552218	NA	1.75E-12	mr1844	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
vg0610552218	NA	4.55E-06	mr1844	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
vg0610552218	NA	1.08E-12	mr1879	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
vg0610552218	6.09E-14	NA	mr1087_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
vg0610552218	3.59E-12	1.16E-20	mr1087_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
vg0610552218	NA	1.06E-07	mr1091_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
vg0610552218	NA	5.51E-06	mr1094_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
vg0610552218	NA	3.05E-06	mr1096_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
vg0610552218	6.30E-06	6.30E-06	mr1474_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
vg0610552218	NA	1.16E-11	mr1844_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
vg0610552218	NA	4.12E-06	mr1844_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