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Detailed information for vg1121176979:

Variant ID: vg1121176979 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21176979
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ACTAGTTTGGCTAAGATCGACCTAAGCCTCAATAACCTGACAGGTGAAATCACAGAGGAACACTTAGCTGGCTTAAAGAGTTTAAAAAGCTTAAACTTGT[A/C]
TTATAATCCCTACTTGAAGATTGTGCTTGGTGATGAATGGTTACCGCCCTTTAGACTAGAGGTGGCGAGATTTGGATCTTGTCAGCTAGGTCCAATGTTT

Reverse complement sequence

AAACATTGGACCTAGCTGACAAGATCCAAATCTCGCCACCTCTAGTCTAAAGGGCGGTAACCATTCATCACCAAGCACAATCTTCAAGTAGGGATTATAA[T/G]
ACAAGTTTAAGCTTTTTAAACTCTTTAAGCCAGCTAAGTGTTCCTCTGTGATTTCACCTGTCAGGTTATTGAGGCTTAGGTCGATCTTAGCCAAACTAGT

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	86.70%	0.50%	1.25%	11.55%	NA
All Indica	2759	80.20%	0.70%	1.23%	17.83%	NA
All Japonica	1512	98.20%	0.10%	0.07%	1.59%	NA
Aus	269	85.50%	0.00%	8.18%	6.32%	NA
Indica I	595	90.40%	0.70%	0.17%	8.74%	NA
Indica II	465	75.30%	1.70%	1.08%	21.94%	NA
Indica III	913	78.90%	0.10%	1.86%	19.17%	NA
Indica Intermediate	786	77.00%	0.90%	1.40%	20.74%	NA
Temperate Japonica	767	97.30%	0.30%	0.00%	2.48%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	85.60%	0.00%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121176979	A -> DEL	LOC_Os11g36020.1	N	frameshift_variant	Average:53.779; most accessible tissue: Callus, score: 85.926	N	N	N	N
vg1121176979	A -> C	LOC_Os11g36020.1	missense_variant ; p.Tyr421Ser; MODERATE	nonsynonymous_codon ; Y421S	Average:53.779; most accessible tissue: Callus, score: 85.926	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121176979	7.05E-07	NA	mr1655	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
vg1121176979	5.25E-06	NA	mr1770	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