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Detailed information for vg1109410881:

Variant ID: vg1109410881 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9410881
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGACGAGCCTCTCCGCCTCCCGCACCACGCCGTCGCGGCTGGCCGCCTCGCCGTCGGCGAAGTACCACCTCCTCATCCAGCTGCCCGTGCGCGGCCTCG[A/G]
CTTGAGCGTCGTCAGCGTGTACCACCGGTCGGTCTTCTCCCGGACGAGCGCCGCCACGTGCGGTGGCACGGCGACGCCGTCCTCGACGTTGCCGAGCTTG

Reverse complement sequence

CAAGCTCGGCAACGTCGAGGACGGCGTCGCCGTGCCACCGCACGTGGCGGCGCTCGTCCGGGAGAAGACCGACCGGTGGTACACGCTGACGACGCTCAAG[T/C]
CGAGGCCGCGCACGGGCAGCTGGATGAGGAGGTGGTACTTCGCCGACGGCGAGGCGGCCAGCCGCGACGGCGTGGTGCGGGAGGCGGAGAGGCTCGTCGG

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	91.70%	7.60%	0.06%	0.57%	NA
All Indica	2759	86.70%	12.70%	0.11%	0.54%	NA
All Japonica	1512	99.10%	0.50%	0.00%	0.46%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	79.80%	17.50%	0.17%	2.52%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	86.20%	13.80%	0.00%	0.00%	NA
Indica Intermediate	786	85.10%	14.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	0.00%	0.00%	1.39%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	4.40%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109410881	A -> DEL	LOC_Os11g16970.1	N	frameshift_variant	Average:78.104; most accessible tissue: Zhenshan97 young leaf, score: 91.232	N	N	N	N
vg1109410881	A -> G	LOC_Os11g16970.1	missense_variant ; p.Ser183Pro; MODERATE	nonsynonymous_codon ; S183P	Average:78.104; most accessible tissue: Zhenshan97 young leaf, score: 91.232	unknown	unknown	TOLERATED	0.24

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109410881	NA	3.79E-07	mr1739	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
vg1109410881	NA	9.03E-06	mr1759	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
vg1109410881	NA	7.98E-07	mr1624_2	Ind_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