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Detailed information for vg0405536257:

Variant ID: vg0405536257 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5536257
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACATGTGTTCCCGGCCACCATGAGTCAATCTATGCCCTCAGCCGCATTAGCAGCAGCGGCGCCACCGGTTTCCCTCACCGCGACTAAGGAGGATGAGGC[C/T]
GACATGGACAAATCTGAGATGAAACCAGAGGAGACATTCCAAGAGTTGTGTGCCAAGATGATTGCCATGCTCAACAACATGCTCGTGACATGCTGCGACA

Reverse complement sequence

TGTCGCAGCATGTCACGAGCATGTTGTTGAGCATGGCAATCATCTTGGCACACAACTCTTGGAATGTCTCCTCTGGTTTCATCTCAGATTTGTCCATGTC[G/A]
GCCTCATCCTCCTTAGTCGCGGTGAGGGAAACCGGTGGCGCCGCTGCTGCTAATGCGGCTGAGGGCATAGATTGACTCATGGTGGCCGGGAACACATGTT

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	33.70%	5.40%	3.66%	57.30%	NA
All Indica	2759	14.70%	9.00%	4.86%	71.51%	NA
All Japonica	1512	67.40%	0.10%	0.46%	32.01%	NA
Aus	269	51.30%	0.00%	6.69%	42.01%	NA
Indica I	595	5.20%	4.20%	3.03%	87.56%	NA
Indica II	465	19.40%	16.10%	6.88%	57.63%	NA
Indica III	913	15.40%	13.50%	5.37%	65.72%	NA
Indica Intermediate	786	18.20%	3.10%	4.45%	74.30%	NA
Temperate Japonica	767	66.00%	0.10%	0.52%	33.38%	NA
Tropical Japonica	504	63.50%	0.00%	0.20%	36.31%	NA
Japonica Intermediate	241	80.10%	0.40%	0.83%	18.67%	NA
VI/Aromatic	96	0.00%	0.00%	9.38%	90.62%	NA
Intermediate	90	33.30%	4.40%	5.56%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405536257	C -> DEL	LOC_Os04g10250.1	N	frameshift_variant	Average:49.642; most accessible tissue: Minghui63 flag leaf, score: 87.98	N	N	N	N
vg0405536257	C -> T	LOC_Os04g10250.1	synonymous_variant ; p.Ala167Ala; LOW	synonymous_codon	Average:49.642; most accessible tissue: Minghui63 flag leaf, score: 87.98	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405536257	NA	1.65E-17	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
vg0405536257	7.41E-08	7.70E-10	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
vg0405536257	1.03E-06	2.92E-18	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
vg0405536257	1.04E-07	1.98E-08	mr1062	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
vg0405536257	6.25E-06	NA	mr1525	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
vg0405536257	2.24E-08	6.99E-09	mr1525	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
vg0405536257	NA	1.64E-14	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
vg0405536257	3.57E-06	1.02E-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
vg0405536257	NA	4.27E-06	mr1631	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
vg0405536257	NA	4.42E-08	mr1806	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
vg0405536257	NA	2.00E-14	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
vg0405536257	4.58E-06	4.58E-06	mr1035_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
vg0405536257	NA	3.83E-19	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
vg0405536257	1.08E-07	5.14E-09	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
vg0405536257	8.30E-07	3.47E-08	mr1525_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
vg0405536257	4.48E-06	7.01E-07	mr1631_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