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Detailed information for vg1105183353:

Variant ID: vg1105183353 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5183353
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.02, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

CCTATATTCAGTTGCTGCCACAATTGACGCCACTCGTAGGGTAGAAGGGGCCAAGAAAGGATTGATAATCTCCACTCCACTTGACGTACCAGAGATGGCT[A/G]
AAACATATGAGCAAGTCACTGGTTTTGAGCTTGGGAAAGAACCCCCGGAGGAGTTGTTTGAGACGTACGACAACTGCTCTCTCATTATGGAAGTTGTTAA

Reverse complement sequence

TTAACAACTTCCATAATGAGAGAGCAGTTGTCGTACGTCTCAAACAACTCCTCCGGGGGTTCTTTCCCAAGCTCAAAACCAGTGACTTGCTCATATGTTT[T/C]
AGCCATCTCTGGTACGTCAAGTGGAGTGGAGATTATCAATCCTTTCTTGGCCCCTTCTACCCTACGAGTGGCGTCAATTGTGGCAGCAACTGAATATAGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.70%	5.40%	0.85%	31.06%	NA
All Indica	2759	49.00%	1.50%	0.98%	48.50%	NA
All Japonica	1512	91.30%	7.50%	0.07%	1.12%	NA
Aus	269	56.10%	10.00%	1.49%	32.34%	NA
Indica I	595	26.60%	1.30%	2.02%	70.08%	NA
Indica II	465	21.10%	0.40%	0.43%	78.06%	NA
Indica III	913	72.00%	1.20%	0.66%	26.18%	NA
Indica Intermediate	786	56.00%	2.50%	0.89%	40.59%	NA
Temperate Japonica	767	89.00%	8.90%	0.13%	1.96%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	80.90%	18.30%	0.00%	0.83%	NA
VI/Aromatic	96	24.00%	68.80%	7.29%	0.00%	NA
Intermediate	90	62.20%	7.80%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105183353	A -> DEL	LOC_Os11g09710.1	N	frameshift_variant	Average:15.54; most accessible tissue: Callus, score: 72.073	N	N	N	N
vg1105183353	A -> G	LOC_Os11g09710.1	missense_variant ; p.Lys143Glu; MODERATE	nonsynonymous_codon ; K143E	Average:15.54; most accessible tissue: Callus, score: 72.073	unknown	unknown	TOLERATED	0.97

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105183353	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
vg1105183353	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