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Detailed information for vg0405464016:

Variant ID: vg0405464016 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5464016
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, C: 0.01, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

AGATGTCATGGCACAGGGCCGGTGTCCTGCTGCTAGGGGCTCAACCTTGGTTACCTGTCTCGGGAATCCTGGCCGTAGCCAGGGTTGGGTTTGTACTCTT[G/A]
TCTATGGCTAGGATGGGTTGGGAACTATGTCACGTCTTCTGTCCGTATGCCGTGGTGGTATGTGGCGCGTGGTTACACGTGAGGAAAACGTGTCTTGTGG

Reverse complement sequence

CCACAAGACACGTTTTCCTCACGTGTAACCACGCGCCACATACCACCACGGCATACGGACAGAAGACGTGACATAGTTCCCAACCCATCCTAGCCATAGA[C/T]
AAGAGTACAAACCCAACCCTGGCTACGGCCAGGATTCCCGAGACAGGTAACCAAGGTTGAGCCCCTAGCAGCAGGACACCGGCCCTGTGCCATGACATCT

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	51.10%	14.00%	3.83%	31.06%	NA
All Indica	2759	31.00%	16.20%	5.73%	47.12%	NA
All Japonica	1512	97.70%	0.80%	0.07%	1.46%	NA
Aus	269	7.40%	48.30%	4.09%	40.15%	NA
Indica I	595	21.70%	2.20%	5.38%	70.76%	NA
Indica II	465	32.70%	38.70%	5.59%	23.01%	NA
Indica III	913	38.20%	12.90%	5.26%	43.59%	NA
Indica Intermediate	786	28.60%	17.20%	6.62%	47.58%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	95.60%	0.60%	0.20%	3.57%	NA
Japonica Intermediate	241	95.40%	2.90%	0.00%	1.66%	NA
VI/Aromatic	96	17.70%	53.10%	9.38%	19.79%	NA
Intermediate	90	52.20%	24.40%	2.22%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405464016	G -> DEL	LOC_Os04g10120.1	N	frameshift_variant	Average:38.924; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0405464016	G -> A	LOC_Os04g10120.1	synonymous_variant ; p.Leu51Leu; LOW	synonymous_codon	Average:38.924; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405464016	NA	1.94E-06	mr1035	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
vg0405464016	NA	8.21E-10	mr1059	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
vg0405464016	3.56E-06	2.60E-09	mr1062	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
vg0405464016	NA	9.64E-07	mr1136	Ind_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
vg0405464016	NA	2.44E-12	mr1143	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
vg0405464016	NA	3.94E-11	mr1167	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
vg0405464016	NA	2.12E-07	mr1458	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
vg0405464016	NA	6.40E-10	mr1535	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
vg0405464016	NA	7.05E-07	mr1626	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
vg0405464016	NA	2.90E-11	mr1675	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
vg0405464016	NA	7.30E-09	mr1726	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
vg0405464016	NA	2.22E-08	mr1950	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
vg0405464016	NA	7.18E-12	mr1969	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
vg0405464016	NA	2.41E-12	mr1995	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
vg0405464016	1.28E-06	3.79E-15	mr1062_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
vg0405464016	NA	2.07E-08	mr1158_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
vg0405464016	NA	3.15E-06	mr1158_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
vg0405464016	NA	5.02E-08	mr1167_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
vg0405464016	NA	5.64E-06	mr1277_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
vg0405464016	NA	1.69E-07	mr1830_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
vg0405464016	NA	6.11E-06	mr1971_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