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Detailed information for vg0139756098:

Variant ID: vg0139756098 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39756098
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.12, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTCACCTCAAGGTTCTGGAAGCAGTTGCATGAAGCCCTCGGAACCGATCTAAACTTTAGTACAGCTTACCATCCGCAGACCGATGGTCAGACAGAAAG[A/G]
GTAAACCAAATCCTAGAAGACATGCTACGTGCGTGTGCCCTGGATTTCGAAGGCACTTGGGATCGTTGTTTGCCGTATGCTGAGTTCTTATACAACAACA

Reverse complement sequence

TGTTGTTGTATAAGAACTCAGCATACGGCAAACAACGATCCCAAGTGCCTTCGAAATCCAGGGCACACGCACGTAGCATGTCTTCTAGGATTTGGTTTAC[T/C]
CTTTCTGTCTGACCATCGGTCTGCGGATGGTAAGCTGTACTAAAGTTTAGATCGGTTCCGAGGGCTTCATGCAACTGCTTCCAGAACCTTGAGGTGAACT

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	27.50%	7.40%	17.69%	47.38%	NA
All Indica	2759	4.00%	12.40%	28.63%	54.98%	NA
All Japonica	1512	75.60%	0.10%	0.60%	23.68%	NA
Aus	269	2.60%	0.00%	8.18%	89.22%	NA
Indica I	595	3.40%	7.60%	16.64%	72.44%	NA
Indica II	465	2.20%	4.10%	23.87%	69.89%	NA
Indica III	913	3.60%	23.30%	41.07%	31.98%	NA
Indica Intermediate	786	6.00%	8.30%	26.08%	59.67%	NA
Temperate Japonica	767	97.80%	0.00%	0.13%	2.09%	NA
Tropical Japonica	504	55.40%	0.20%	0.60%	43.85%	NA
Japonica Intermediate	241	47.30%	0.40%	2.07%	50.21%	NA
VI/Aromatic	96	2.10%	1.00%	7.29%	89.58%	NA
Intermediate	90	44.40%	4.40%	8.89%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0139756098	A -> G	LOC_Os01g68410.1	splice_region_variant&synonymous_variant ; p.Arg1336Arg; LOW	synonymous_codon	Average:14.469; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0139756098	A -> DEL	LOC_Os01g68410.1	N	frameshift_variant	Average:14.469; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0139756098	NA	1.59E-07	mr1114	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
vg0139756098	8.05E-07	9.94E-08	mr1116	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
vg0139756098	2.60E-08	1.21E-09	mr1117	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
vg0139756098	4.85E-08	5.63E-10	mr1119	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
vg0139756098	8.52E-07	4.49E-08	mr1120	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
vg0139756098	NA	1.54E-06	mr1247	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
vg0139756098	1.76E-06	7.36E-08	mr1496	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
vg0139756098	NA	2.53E-06	mr1113_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
vg0139756098	8.08E-07	4.39E-08	mr1114_2	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
vg0139756098	3.41E-08	1.05E-09	mr1117_2	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
vg0139756098	1.65E-06	4.29E-08	mr1119_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
vg0139756098	3.25E-06	2.97E-06	mr1120_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
vg0139756098	2.63E-06	1.07E-07	mr1240_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
vg0139756098	4.46E-06	1.14E-06	mr1247_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
vg0139756098	2.67E-07	1.61E-08	mr1496_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