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Detailed information for vg0405445291:

Variant ID: vg0405445291 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5445291
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CCCAGAAATTCCTTTCTGGAGATCGATTTTACAGGAATCGTGAAAACCAAGAAATGTACTCAAGCCTTTCCATGTGAGCGTGAACTCCTTACGAAAAAAG[C/T]
GAAAAGAAATACCATCTTCTATTTCTTTCAAAGTGCACAGAAATTGCAAAGTACGCAAAGGAGAACCAGGCTCATCTACCACAGCAAATCTCTGCCAACC

Reverse complement sequence

GGTTGGCAGAGATTTGCTGTGGTAGATGAGCCTGGTTCTCCTTTGCGTACTTTGCAATTTCTGTGCACTTTGAAAGAAATAGAAGATGGTATTTCTTTTC[G/A]
CTTTTTTCGTAAGGAGTTCACGCTCACATGGAAAGGCTTGAGTACATTTCTTGGTTTTCACGATTCCTGTAAAATCGATCTCCAGAAAGGAATTTCTGGG

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	57.80%	8.20%	4.87%	29.16%	NA
All Indica	2759	47.20%	1.00%	7.87%	43.89%	NA
All Japonica	1512	76.20%	22.50%	0.00%	1.32%	NA
Aus	269	56.10%	0.00%	2.23%	41.64%	NA
Indica I	595	27.10%	0.00%	8.57%	64.37%	NA
Indica II	465	68.60%	0.20%	3.66%	27.53%	NA
Indica III	913	49.30%	2.60%	9.64%	38.44%	NA
Indica Intermediate	786	47.50%	0.40%	7.76%	44.40%	NA
Temperate Japonica	767	74.20%	25.80%	0.00%	0.00%	NA
Tropical Japonica	504	72.80%	24.00%	0.00%	3.17%	NA
Japonica Intermediate	241	89.60%	8.70%	0.00%	1.66%	NA
VI/Aromatic	96	66.70%	8.30%	4.17%	20.83%	NA
Intermediate	90	68.90%	11.10%	3.33%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405445291	C -> DEL	LOC_Os04g10080.1	N	frameshift_variant	Average:18.943; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0405445291	C -> T	LOC_Os04g10080.1	missense_variant ; p.Arg46His; MODERATE	nonsynonymous_codon ; R46H	Average:18.943; most accessible tissue: Minghui63 young leaf, score: 32.638	benign	0.124	TOLERATED	0.19

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405445291	6.55E-07	NA	mr1035	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
vg0405445291	5.90E-06	1.03E-06	mr1035	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
vg0405445291	1.43E-09	NA	mr1062	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
vg0405445291	6.92E-06	3.84E-10	mr1062	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
vg0405445291	4.21E-10	5.97E-11	mr1525	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
vg0405445291	3.21E-08	3.21E-08	mr1525	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
vg0405445291	8.63E-08	NA	mr1626	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
vg0405445291	7.34E-07	2.97E-08	mr1626	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
vg0405445291	3.55E-06	NA	mr1631	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
vg0405445291	1.75E-06	1.75E-06	mr1631	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
vg0405445291	1.35E-08	NA	mr1035_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
vg0405445291	2.04E-06	3.79E-08	mr1035_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
vg0405445291	1.64E-14	NA	mr1062_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
vg0405445291	1.56E-09	9.12E-13	mr1062_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
vg0405445291	5.33E-11	5.34E-11	mr1525_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
vg0405445291	8.17E-08	8.17E-08	mr1525_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
vg0405445291	1.23E-12	NA	mr1631_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
vg0405445291	1.55E-09	6.10E-13	mr1631_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