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Detailed information for vg1116232716:

Variant ID: vg1116232716 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16232716
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.62, C: 0.37, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTTACAATGGCGAACTGCCTCCCCGTGCGAATCCTCAAAAGGCCGACGACGAGGCAGGGCCTTCGCGAAAGTGGATGCGTGGACAAGTGAAGCTTGCC[A/C]
CCAGGAAGCGAAGGGTTCCTGCTTCGTCTGACTCCGACACCGACGACGAGGATGATGCCGAAGAACGTGACGGCGAGGAGGAAGGAGAGGAAGAGGAGGA

Reverse complement sequence

TCCTCCTCTTCCTCTCCTTCCTCCTCGCCGTCACGTTCTTCGGCATCATCCTCGTCGTCGGTGTCGGAGTCAGACGAAGCAGGAACCCTTCGCTTCCTGG[T/G]
GGCAAGCTTCACTTGTCCACGCATCCACTTTCGCGAAGGCCCTGCCTCGTCGTCGGCCTTTTGAGGATTCGCACGGGGAGGCAGTTCGCCATTGTAAACT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.90%	34.60%	1.35%	0.11%	NA
All Indica	2759	97.80%	1.80%	0.14%	0.18%	NA
All Japonica	1512	3.60%	96.40%	0.00%	0.00%	NA
Aus	269	76.20%	1.50%	22.30%	0.00%	NA
Indica I	595	96.60%	2.40%	0.50%	0.50%	NA
Indica II	465	99.60%	0.20%	0.00%	0.22%	NA
Indica III	913	99.50%	0.30%	0.11%	0.11%	NA
Indica Intermediate	786	95.80%	4.20%	0.00%	0.00%	NA
Temperate Japonica	767	3.40%	96.60%	0.00%	0.00%	NA
Tropical Japonica	504	4.40%	95.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	58.90%	41.10%	0.00%	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
vg1116232716	A -> DEL	LOC_Os11g28230.1	N	frameshift_variant	Average:41.196; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg1116232716	A -> C	LOC_Os11g28230.1	missense_variant ; p.Thr485Pro; MODERATE	nonsynonymous_codon ; T485P	Average:41.196; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	possibly damaging	-1.867	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116232716	9.47E-07	NA	mr1164	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
vg1116232716	NA	1.78E-23	mr1383	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
vg1116232716	NA	3.14E-17	mr1566	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
vg1116232716	NA	1.42E-57	mr1594	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
vg1116232716	NA	2.01E-08	mr1595	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
vg1116232716	NA	1.32E-35	mr1682	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
vg1116232716	NA	6.24E-19	mr1754	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
vg1116232716	4.04E-09	1.01E-107	mr1758	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
vg1116232716	9.57E-06	9.57E-06	mr1758	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
vg1116232716	3.75E-08	4.91E-148	mr1758_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
vg1116232716	NA	1.46E-08	mr1758_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
vg1116232716	NA	2.97E-06	mr1795_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