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Detailed information for vg0232791648:

Variant ID: vg0232791648 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32791648
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.25, A: 0.05, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGAGACTGCATCTCCTCCTGCATAGCTGAGATCCACTTCTCACGGTCTCCAGAAACAACAGCTTCAGTGTATGTGGCTGGCTCAAGAGTATTCTCCAC[T/C]
TGTTCAGCACAACTAAAAGCATAATAAACCATATCACATTCCTCAATAAAACGGACTGGAGCTCCACAACTCCTCTTTGTTCTGCGATGGGCAATAGGTT

Reverse complement sequence

AACCTATTGCCCATCGCAGAACAAAGAGGAGTTGTGGAGCTCCAGTCCGTTTTATTGAGGAATGTGATATGGTTTATTATGCTTTTAGTTGTGCTGAACA[A/G]
GTGGAGAATACTCTTGAGCCAGCCACATACACTGAAGCTGTTGTTTCTGGAGACCGTGAGAAGTGGATCTCAGCTATGCAGGAGGAGATGCAGTCTCTTG

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	71.60%	26.50%	1.86%	0.02%	NA
All Indica	2759	96.90%	1.60%	1.45%	0.04%	NA
All Japonica	1512	23.10%	76.80%	0.07%	0.00%	NA
Aus	269	86.20%	1.50%	12.27%	0.00%	NA
Indica I	595	98.00%	1.00%	0.84%	0.17%	NA
Indica II	465	95.50%	2.80%	1.72%	0.00%	NA
Indica III	913	96.70%	1.90%	1.42%	0.00%	NA
Indica Intermediate	786	97.20%	1.00%	1.78%	0.00%	NA
Temperate Japonica	767	42.50%	57.50%	0.00%	0.00%	NA
Tropical Japonica	504	0.00%	100.00%	0.00%	0.00%	NA
Japonica Intermediate	241	10.00%	89.60%	0.41%	0.00%	NA
VI/Aromatic	96	86.50%	1.00%	12.50%	0.00%	NA
Intermediate	90	50.00%	47.80%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0232791648	T -> DEL	LOC_Os02g53610.1	N	frameshift_variant	Average:9.513; most accessible tissue: Callus, score: 14.769	N	N	N	N
vg0232791648	T -> C	LOC_Os02g53610.1	synonymous_variant ; p.Gln463Gln; LOW	synonymous_codon	Average:9.513; most accessible tissue: Callus, score: 14.769	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232791648	NA	1.29E-16	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
vg0232791648	NA	1.08E-15	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
vg0232791648	NA	2.58E-06	mr1510	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
vg0232791648	NA	5.19E-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
vg0232791648	NA	2.24E-12	mr1905	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
vg0232791648	2.69E-09	1.92E-29	mr1062_2	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
vg0232791648	1.63E-06	8.95E-10	mr1062_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
vg0232791648	NA	1.27E-07	mr1418_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
vg0232791648	NA	7.98E-07	mr1488_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
vg0232791648	NA	1.09E-10	mr1506_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
vg0232791648	NA	2.54E-07	mr1683_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
vg0232791648	NA	1.59E-07	mr1765_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
vg0232791648	NA	1.74E-07	mr1824_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
vg0232791648	NA	3.82E-13	mr1838_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