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Detailed information for vg1123808247:

Variant ID: vg1123808247 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23808247
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CGAACAACTAAGGCAACCGCGGAGGGTCAAGCTTTGGAGAGTTCATGAGGACCAAGCCACCCACATTCGCCACAGCTGAAGAACCTATGGATGCTGAAGA[T/C]
TGTTTGAGGGTCATTGAGAAAAAGCTAACTCTTGTTCGAGTACGTGAGGCCGATAAAGTGATCTTTGCGGCAAACCAATTGGAAGGACCAGCCGGAGACT

Reverse complement sequence

AGTCTCCGGCTGGTCCTTCCAATTGGTTTGCCGCAAAGATCACTTTATCGGCCTCACGTACTCGAACAAGAGTTAGCTTTTTCTCAATGACCCTCAAACA[A/G]
TCTTCAGCATCCATAGGTTCTTCAGCTGTGGCGAATGTGGGTGGCTTGGTCCTCATGAACTCTCCAAAGCTTGACCCTCCGCGGTTGCCTTAGTTGTTCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.80%	34.00%	15.28%	7.93%	NA
All Indica	2759	59.80%	20.40%	17.51%	2.36%	NA
All Japonica	1512	14.70%	55.10%	9.85%	20.37%	NA
Aus	269	44.20%	39.00%	16.73%	0.00%	NA
Indica I	595	45.50%	37.50%	16.13%	0.84%	NA
Indica II	465	54.80%	23.40%	16.99%	4.73%	NA
Indica III	913	76.60%	4.10%	16.87%	2.52%	NA
Indica Intermediate	786	53.90%	24.60%	19.59%	1.91%	NA
Temperate Japonica	767	5.10%	57.50%	5.87%	31.55%	NA
Tropical Japonica	504	24.00%	58.10%	12.90%	4.96%	NA
Japonica Intermediate	241	25.70%	41.10%	16.18%	17.01%	NA
VI/Aromatic	96	7.30%	65.60%	27.08%	0.00%	NA
Intermediate	90	30.00%	46.70%	21.11%	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
vg1123808247	T -> DEL	LOC_Os11g39950.1	N	frameshift_variant	Average:41.652; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg1123808247	T -> C	LOC_Os11g39950.1	synonymous_variant ; p.Asp411Asp; LOW	synonymous_codon	Average:41.652; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123808247	NA	6.50E-06	mr1177	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
vg1123808247	NA	6.91E-06	mr1745	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
vg1123808247	5.91E-07	5.91E-07	mr1953	Ind_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