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Detailed information for vg0128511406:

Variant ID: vg0128511406 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28511406
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GACTGGTATATAAACTTGACAATAACGTGCATTTTAGTCAAAAACATTGATGCATACATTTGATTAATCCTGGTATTGCTAGATCATTGACTGATGGATT[T/C]
AATTTCGTGTTCTGCCATGTTCATAACTCGAGATAATGAATATGTTGATTAATCGAATCGCTCGGAAATTATGTTATTTGCATGTACTTACTTTTGATAA

Reverse complement sequence

TTATCAAAAGTAAGTACATGCAAATAACATAATTTCCGAGCGATTCGATTAATCAACATATTCATTATCTCGAGTTATGAACATGGCAGAACACGAAATT[A/G]
AATCCATCAGTCAATGATCTAGCAATACCAGGATTAATCAAATGTATGCATCAATGTTTTTGACTAAAATGCACGTTATTGTCAAGTTTATATACCAGTC

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	48.90%	27.20%	0.63%	23.30%	NA
All Indica	2759	72.30%	3.50%	0.62%	23.56%	NA
All Japonica	1512	18.30%	75.10%	0.33%	6.28%	NA
Aus	269	0.00%	3.70%	2.23%	94.05%	NA
Indica I	595	54.30%	3.90%	1.18%	40.67%	NA
Indica II	465	97.20%	1.70%	0.00%	1.08%	NA
Indica III	913	71.60%	5.30%	0.22%	22.89%	NA
Indica Intermediate	786	72.00%	2.30%	1.02%	24.68%	NA
Temperate Japonica	767	0.50%	99.20%	0.00%	0.26%	NA
Tropical Japonica	504	50.00%	32.30%	0.60%	17.06%	NA
Japonica Intermediate	241	8.30%	88.00%	0.83%	2.90%	NA
VI/Aromatic	96	4.20%	13.50%	1.04%	81.25%	NA
Intermediate	90	38.90%	32.20%	1.11%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0128511406	T -> DEL	N	N	silent_mutation	Average:27.499; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0128511406	T -> C	LOC_Os01g49570.1	upstream_gene_variant ; 1833.0bp to feature; MODIFIER	silent_mutation	Average:27.499; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0128511406	T -> C	LOC_Os01g49580.1	upstream_gene_variant ; 1691.0bp to feature; MODIFIER	silent_mutation	Average:27.499; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0128511406	T -> C	LOC_Os01g49570-LOC_Os01g49580	intergenic_region ; MODIFIER	silent_mutation	Average:27.499; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0128511406	NA	2.74E-06	mr1047	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
vg0128511406	NA	2.58E-09	mr1457	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
vg0128511406	NA	6.81E-08	mr1471	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
vg0128511406	NA	1.36E-07	mr1543	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
vg0128511406	NA	2.33E-07	mr1642	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
vg0128511406	NA	3.22E-10	mr1720	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
vg0128511406	NA	8.91E-09	mr1742	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
vg0128511406	9.53E-06	9.52E-06	mr1815	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
vg0128511406	NA	4.33E-20	mr1352_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
vg0128511406	NA	1.76E-08	mr1364_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
vg0128511406	NA	7.18E-08	mr1376_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
vg0128511406	NA	3.51E-08	mr1431_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
vg0128511406	NA	1.02E-10	mr1471_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
vg0128511406	NA	2.17E-10	mr1642_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
vg0128511406	NA	1.93E-07	mr1807_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
vg0128511406	NA	1.35E-07	mr1808_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