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Detailed information for vg1113044398:

Variant ID: vg1113044398 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13044398
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCATCAAACGAAGTACACAAAGGATCTTTTGAGACGGTTCAAGATGGAGAATTGTAAGCCAATTTCAACACCAATTGGTTCTACAGCTATGTTGGATCCT[G/A]
ATGAAGATGGTGAAGCTGTTGATCAAAAGGAGTATAGAAGTATGATTGGATCTTTGTTGTATCTAACTGCTTCTAGGCCAGACATACAATTTGCTGTGTG

Reverse complement sequence

CACACAGCAAATTGTATGTCTGGCCTAGAAGCAGTTAGATACAACAAAGATCCAATCATACTTCTATACTCCTTTTGATCAACAGCTTCACCATCTTCAT[C/T]
AGGATCCAACATAGCTGTAGAACCAATTGGTGTTGAAATTGGCTTACAATTCTCCATCTTGAACCGTCTCAAAAGATCCTTTGTGTACTTCGTTTGATGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.60%	3.50%	14.79%	1.18%	NA
All Indica	2759	68.90%	5.50%	23.70%	1.85%	NA
All Japonica	1512	98.60%	0.20%	0.99%	0.20%	NA
Aus	269	93.30%	2.20%	4.46%	0.00%	NA
Indica I	595	63.90%	2.90%	30.92%	2.35%	NA
Indica II	465	63.20%	7.50%	29.03%	0.22%	NA
Indica III	913	77.40%	5.30%	14.68%	2.63%	NA
Indica Intermediate	786	66.30%	6.60%	25.57%	1.53%	NA
Temperate Japonica	767	98.70%	0.10%	0.91%	0.26%	NA
Tropical Japonica	504	98.00%	0.40%	1.39%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	75.60%	3.30%	18.89%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1113044398	G -> A	LOC_Os11g22670.1	missense_variant ; p.Asp1195Asn; MODERATE	nonsynonymous_codon ; D1195K	Average:8.121; most accessible tissue: Minghui63 panicle, score: 16.27	possibly damaging	1.895	DELETERIOUS	0.00
vg1113044398	G -> A	LOC_Os11g22670.1	missense_variant ; p.Asp1195Asn; MODERATE	nonsynonymous_codon ; D1195N	Average:8.121; most accessible tissue: Minghui63 panicle, score: 16.27	benign	0.753	DELETERIOUS	0.04
vg1113044398	G -> DEL	LOC_Os11g22670.1	N	frameshift_variant	Average:8.121; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113044398	NA	2.67E-06	mr1929_2	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