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Detailed information for vg1124026214:

Variant ID: vg1124026214 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24026214
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGCTGAACACACAAACGGTAAGATCCTAGAAGCACTAAAAAAAGGCTTGAGGGGGCAGCGAAGGGCAAATGGCCAGAGGAGATGCTATCTGTTCTCTGG[G/A]
CCCTTCGAACGACCCCCACAAGACCAACCAAGTTCAGCCCGTTCATGCTTATTTATGGCGATGAGGCAATGACCCCGACAGAGCTAGGGGCTAACTCACC

Reverse complement sequence

GGTGAGTTAGCCCCTAGCTCTGTCGGGGTCATTGCCTCATCGCCATAAATAAGCATGAACGGGCTGAACTTGGTTGGTCTTGTGGGGGTCGTTCGAAGGG[C/T]
CCAGAGAACAGATAGCATCTCCTCTGGCCATTTGCCCTTCGCTGCCCCCTCAAGCCTTTTTTTAGTGCTTCTAGGATCTTACCGTTTGTGTGTTCAGCCG

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	76.90%	8.00%	5.21%	9.90%	NA
All Indica	2759	78.30%	13.10%	8.01%	0.65%	NA
All Japonica	1512	68.80%	0.70%	1.32%	29.23%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	52.80%	31.80%	12.61%	2.86%	NA
Indica II	465	82.60%	9.00%	8.39%	0.00%	NA
Indica III	913	87.70%	6.40%	5.91%	0.00%	NA
Indica Intermediate	786	84.00%	9.20%	6.74%	0.13%	NA
Temperate Japonica	767	69.50%	0.80%	0.65%	29.07%	NA
Tropical Japonica	504	75.20%	0.00%	1.59%	23.21%	NA
Japonica Intermediate	241	53.10%	1.70%	2.90%	42.32%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	87.80%	3.30%	4.44%	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
vg1124026214	G -> A	LOC_Os11g40284.1	3_prime_UTR_variant ; 868.0bp to feature; MODIFIER	silent_mutation	Average:15.872; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1124026214	G -> A	LOC_Os11g40300.1	downstream_gene_variant ; 1782.0bp to feature; MODIFIER	silent_mutation	Average:15.872; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1124026214	G -> DEL	N	N	silent_mutation	Average:15.872; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124026214	4.46E-06	NA	mr1842	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