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Detailed information for vg0608522054:

Variant ID: vg0608522054 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8522054
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.30, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTAAGGTCAACCGTTGTCATCGCACTGTCATCAATCGTTATGCCTCCACCAATCAACCTAACCCATTGGCACCGGAACAGAGGGACCTTGAGAGGACC[G/A]
TAGTCAAGTTCCCATATATCCTCGATGGCACCGTAATACGTGCCAGTTGTTCCATCGTGTCCCATGGCATCGATACGAACAACGCTGTTTTGGTTCGTGC

Reverse complement sequence

GCACGAACCAAAACAGCGTTGTTCGTATCGATGCCATGGGACACGATGGAACAACTGGCACGTATTACGGTGCCATCGAGGATATATGGGAACTTGACTA[C/T]
GGTCCTCTCAAGGTCCCTCTGTTCCGGTGCCAATGGGTTAGGTTGATTGGTGGAGGCATAACGATTGATGACAGTGCGATGACAACGGTTGACCTTAACA

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	42.70%	3.00%	35.15%	19.23%	NA
All Indica	2759	8.00%	4.70%	55.85%	31.39%	NA
All Japonica	1512	93.50%	0.50%	5.95%	0.13%	NA
Aus	269	86.20%	0.00%	1.12%	12.64%	NA
Indica I	595	8.40%	6.20%	47.23%	38.15%	NA
Indica II	465	8.20%	6.70%	69.89%	15.27%	NA
Indica III	913	6.80%	1.40%	48.30%	43.48%	NA
Indica Intermediate	786	9.20%	6.20%	62.85%	21.76%	NA
Temperate Japonica	767	88.10%	0.90%	10.82%	0.13%	NA
Tropical Japonica	504	99.20%	0.00%	0.60%	0.20%	NA
Japonica Intermediate	241	98.30%	0.00%	1.66%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	61.10%	3.30%	28.89%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608522054	G -> A	LOC_Os06g15030.1	synonymous_variant ; p.Tyr342Tyr; LOW	synonymous_codon	Average:6.915; most accessible tissue: Callus, score: 24.406	N	N	N	N
vg0608522054	G -> DEL	LOC_Os06g15030.1	N	frameshift_variant	Average:6.915; most accessible tissue: Callus, score: 24.406	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608522054	NA	2.92E-09	mr1342	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
vg0608522054	NA	3.88E-08	mr1648	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
vg0608522054	NA	8.63E-07	mr1652	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
vg0608522054	NA	7.48E-13	mr1655	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
vg0608522054	NA	2.65E-06	mr1748	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
vg0608522054	NA	1.20E-09	mr1011_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
vg0608522054	NA	3.48E-06	mr1053_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
vg0608522054	NA	5.58E-63	mr1068_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
vg0608522054	NA	1.58E-39	mr1110_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
vg0608522054	NA	4.37E-13	mr1147_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
vg0608522054	NA	2.42E-25	mr1244_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
vg0608522054	NA	9.36E-06	mr1329_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
vg0608522054	NA	2.41E-23	mr1551_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
vg0608522054	NA	2.41E-15	mr1552_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
vg0608522054	2.32E-06	NA	mr1574_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
vg0608522054	NA	2.17E-06	mr1754_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
vg0608522054	NA	2.62E-07	mr1819_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
vg0608522054	NA	1.43E-15	mr1938_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
vg0608522054	NA	4.28E-06	mr1982_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