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Detailed information for vg0507139485:

Variant ID: vg0507139485 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7139485
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, A: 0.25, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

TAGGTATAAAGCTAGTTATTCCGGATCGTGGTTCTATGATTGCTCGGTGTGACGGATCGGAGTCCGGGAGGCTTCGGATTGTTCTCACCCTCACCACTTC[A/G]
TCGCATCCGACCTTGGTAGGTATAAAGATAGTTATCCTCTTGCTGCTCGTAGCTAGTTACCCTCTTGTGTTTCGGTTTACGCCGGCACTCTGTCTTGAAC

Reverse complement sequence

GTTCAAGACAGAGTGCCGGCGTAAACCGAAACACAAGAGGGTAACTAGCTACGAGCAGCAAGAGGATAACTATCTTTATACCTACCAAGGTCGGATGCGA[T/C]
GAAGTGGTGAGGGTGAGAACAATCCGAAGCCTCCCGGACTCCGATCCGTCACACCGAGCAATCATAGAACCACGATCCGGAATAACTAGCTTTATACCTA

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	58.50%	40.80%	0.06%	0.61%	NA
All Indica	2759	40.30%	58.90%	0.04%	0.80%	NA
All Japonica	1512	95.80%	3.90%	0.07%	0.26%	NA
Aus	269	20.10%	79.90%	0.00%	0.00%	NA
Indica I	595	18.00%	82.00%	0.00%	0.00%	NA
Indica II	465	74.00%	25.20%	0.00%	0.86%	NA
Indica III	913	40.50%	58.30%	0.11%	1.10%	NA
Indica Intermediate	786	36.90%	62.10%	0.00%	1.02%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	95.00%	4.20%	0.20%	0.60%	NA
Japonica Intermediate	241	85.50%	14.10%	0.00%	0.41%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	66.70%	30.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507139485	A -> DEL	LOC_Os05g12420.1	N	frameshift_variant	Average:56.699; most accessible tissue: Minghui63 young leaf, score: 76.82	N	N	N	N
vg0507139485	A -> G	LOC_Os05g12420.1	synonymous_variant ; p.Ser136Ser; LOW	synonymous_codon	Average:56.699; most accessible tissue: Minghui63 young leaf, score: 76.82	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507139485	NA	8.80E-09	mr1050	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
vg0507139485	3.32E-06	2.50E-11	mr1195	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
vg0507139485	2.43E-07	4.87E-10	mr1195	Ind_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
vg0507139485	NA	3.23E-12	mr1272	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
vg0507139485	2.77E-07	NA	mr1531	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
vg0507139485	6.14E-08	7.12E-12	mr1531	Ind_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
vg0507139485	1.03E-35	7.59E-30	mr1593	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
vg0507139485	1.21E-43	1.02E-75	mr1593	Ind_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
vg0507139485	NA	2.84E-12	mr1904	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
vg0507139485	3.22E-11	1.26E-32	mr1195_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
vg0507139485	3.87E-12	3.32E-23	mr1195_2	Ind_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
vg0507139485	NA	2.78E-09	mr1378_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
vg0507139485	NA	7.18E-10	mr1482_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
vg0507139485	NA	2.04E-07	mr1482_2	Ind_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
vg0507139485	1.20E-09	NA	mr1531_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
vg0507139485	6.39E-10	1.26E-14	mr1531_2	Ind_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
vg0507139485	2.02E-41	2.19E-38	mr1593_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
vg0507139485	1.13E-51	1.87E-94	mr1593_2	Ind_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
vg0507139485	NA	2.69E-08	mr1748_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
vg0507139485	1.06E-06	3.22E-11	mr1807_2	Ind_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
vg0507139485	NA	1.39E-06	mr1977_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