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Detailed information for vg1120961872:

Variant ID: vg1120961872 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20961872
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTACCTGGTTTAAGTCCTAGACTTGATACGGGTGCTCGCATTTACGGCTAAATATTCTTTCAATGGTAGGTGGCGTACCCGTCAACAGCGAGACGCCTGT[G/A]
GTGACATCGTCATTCTCAAAATGTGTTGGCTCAGTCTTTTAGAGGTACTCAAAGGAGCAGGCTGTGCGCGTGTCGTGTTTCTTAAAAAAAAATCCAATAT

Reverse complement sequence

ATATTGGATTTTTTTTTAAGAAACACGACACGCGCACAGCCTGCTCCTTTGAGTACCTCTAAAAGACTGAGCCAACACATTTTGAGAATGACGATGTCAC[C/T]
ACAGGCGTCTCGCTGTTGACGGGTACGCCACCTACCATTGAAAGAATATTTAGCCGTAAATGCGAGCACCCGTATCAAGTCTAGGACTTAAACCAGGTAG

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	95.50%	2.40%	1.57%	0.49%	NA
All Indica	2759	93.10%	4.20%	2.57%	0.11%	NA
All Japonica	1512	98.70%	0.00%	0.07%	1.26%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	71.40%	17.50%	11.09%	0.00%	NA
Indica II	465	99.40%	0.20%	0.22%	0.22%	NA
Indica III	913	99.60%	0.10%	0.22%	0.11%	NA
Indica Intermediate	786	98.50%	1.10%	0.25%	0.13%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	96.20%	0.00%	0.20%	3.57%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120961872	G -> A	LOC_Os11g35720.1	missense_variant ; p.Gly100Ser; MODERATE	nonsynonymous_codon ; G100S	Average:34.547; most accessible tissue: Zhenshan97 young leaf, score: 52.657	unknown	unknown	DELETERIOUS	0.00
vg1120961872	G -> DEL	LOC_Os11g35720.1	N	frameshift_variant	Average:34.547; most accessible tissue: Zhenshan97 young leaf, score: 52.657	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120961872	NA	7.86E-06	mr1662_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
vg1120961872	5.50E-07	2.04E-08	mr1742_2	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