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Detailed information for vg0409515411:

Variant ID: vg0409515411 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 9515411
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.56, A: 0.44, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTAGGCACTACTTTCTTGTTATAATGCCTAGCAACTCGTTCCTTATCTCTGGTAACCTTAGCAAGGGCTCGTAAACGCGATTGAACCAAGTCCTCCCT[C/A]
TCATCGGCCATAAGGTTATAATATTCATCGGCTATCAAACCGTCTTGCAATTCTATCCTTCTAGAGCCGATTCTAACTTCCCATGGCAAAACAGCTTCAT

Reverse complement sequence

ATGAAGCTGTTTTGCCATGGGAAGTTAGAATCGGCTCTAGAAGGATAGAATTGCAAGACGGTTTGATAGCCGATGAATATTATAACCTTATGGCCGATGA[G/T]
AGGGAGGACTTGGTTCAATCGCGTTTACGAGCCCTTGCTAAGGTTACCAGAGATAAGGAACGAGTTGCTAGGCATTATAACAAGAAAGTAGTGCCTAAGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.50%	25.50%	2.24%	7.70%	NA
All Indica	2759	96.90%	2.30%	0.72%	0.07%	NA
All Japonica	1512	2.60%	72.60%	2.51%	22.35%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	97.20%	1.90%	0.43%	0.43%	NA
Indica III	913	94.30%	4.10%	1.64%	0.00%	NA
Indica Intermediate	786	98.10%	1.50%	0.38%	0.00%	NA
Temperate Japonica	767	0.80%	97.80%	0.13%	1.30%	NA
Tropical Japonica	504	4.20%	32.70%	6.35%	56.75%	NA
Japonica Intermediate	241	5.00%	75.50%	2.07%	17.43%	NA
VI/Aromatic	96	21.90%	11.50%	44.79%	21.88%	NA
Intermediate	90	53.30%	37.80%	5.56%	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
vg0409515411	C -> DEL	LOC_Os04g17380.1	N	frameshift_variant	Average:19.291; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0409515411	C -> A	LOC_Os04g17380.1	missense_variant ; p.Glu65Asp; MODERATE	nonsynonymous_codon ; E65D	Average:19.291; most accessible tissue: Minghui63 panicle, score: 25.313	benign	0.537	DELETERIOUS	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0409515411	NA	7.90E-07	mr1040	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
vg0409515411	NA	5.61E-08	mr1045	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
vg0409515411	NA	9.55E-08	mr1206	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
vg0409515411	NA	4.17E-08	mr1229	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
vg0409515411	NA	1.66E-07	mr1403	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
vg0409515411	NA	1.86E-09	mr1663	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
vg0409515411	NA	7.59E-07	mr1668	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
vg0409515411	NA	7.67E-07	mr1739	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
vg0409515411	NA	4.20E-09	mr1746	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
vg0409515411	NA	5.80E-07	mr1785	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
vg0409515411	NA	1.37E-13	mr1982	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
vg0409515411	NA	1.64E-15	mr1301_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
vg0409515411	NA	1.14E-50	mr1991_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
vg0409515411	NA	1.97E-07	mr1991_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