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Detailed information for vg1105183067:

Variant ID: vg1105183067 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5183067
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.02, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTCTCTTGTGTAGAATGATGCTGCTTATGAGTGGAGAATTACCCAATGCCTGATCAATGGAGTTTCGTTGGACTTCAAGGTTTATGACCAAAATCGTA[A/C]
ACGTACGTAATTCTTTCTCGTTTTCTTTTCTCTCTGTCTGTTCTTTATTTTCTTTCACATCTTTCCGTCCTTTCATTTTAACTCTTTTTTGGGTCTCGGT

Reverse complement sequence

ACCGAGACCCAAAAAAGAGTTAAAATGAAAGGACGGAAAGATGTGAAAGAAAATAAAGAACAGACAGAGAGAAAAGAAAACGAGAAAGAATTACGTACGT[T/G]
TACGATTTTGGTCATAAACCTTGAAGTCCAACGAAACTCCATTGATCAGGCATTGGGTAATTCTCCACTCATAAGCAGCATCATTCTACACAAGAGAGGT

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	62.80%	5.30%	0.74%	31.15%	NA
All Indica	2759	49.00%	1.50%	1.20%	48.35%	NA
All Japonica	1512	91.40%	7.40%	0.00%	1.19%	NA
Aus	269	56.90%	10.00%	0.74%	32.34%	NA
Indica I	595	26.10%	1.30%	1.51%	71.09%	NA
Indica II	465	20.60%	0.40%	1.72%	77.20%	NA
Indica III	913	72.50%	1.30%	0.66%	25.52%	NA
Indica Intermediate	786	55.70%	2.40%	1.27%	40.59%	NA
Temperate Japonica	767	89.00%	8.90%	0.00%	2.09%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	81.30%	17.80%	0.00%	0.83%	NA
VI/Aromatic	96	24.00%	67.70%	0.00%	8.33%	NA
Intermediate	90	64.40%	7.80%	0.00%	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
vg1105183067	A -> DEL	LOC_Os11g09710.1	N	frameshift_variant	Average:11.644; most accessible tissue: Callus, score: 71.063	N	N	N	N
vg1105183067	A -> C	LOC_Os11g09710.1	missense_variant&splice_region_variant ; p.Lys105Thr; MODERATE	nonsynonymous_codon ; K105T	Average:11.644; most accessible tissue: Callus, score: 71.063	benign	0.415	TOLERATED	0.07

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105183067	NA	7.24E-06	mr1280	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
vg1105183067	NA	6.22E-06	mr1280	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