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Detailed information for vg1108752863:

Variant ID: vg1108752863 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8752863
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACTTTTAAATTGTGCTTGTTTTCTTTATCTTTGTCTGGTACTGCTTTTACATGGTTTACTTCTTTACCGGCAAATTCTATTCATACTTGGCCTCAATTA[G/C]
AGCAAAGATTTCATGATTATTTCTATACTGGTGAAATTGAACTTAGGCTATGATTTGACGTTGATTAAGCAAAAGTACAATGAATCTGTCATTATTGATT

Reverse complement sequence

AATCAATAATGACAGATTCATTGTACTTTTGCTTAATCAACGTCAAATCATAGCCTAAGTTCAATTTCACCAGTATAGAAATAATCATGAAATCTTTGCT[C/G]
TAATTGAGGCCAAGTATGAATAGAATTTGCCGGTAAAGAAGTAAACCATGTAAAAGCAGTACCAGACAAAGATAAAGAAAACAAGCACAATTTAAAAGTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.30%	10.00%	4.78%	10.96%	NA
All Indica	2759	60.70%	16.50%	6.92%	15.95%	NA
All Japonica	1512	95.10%	0.40%	1.12%	3.37%	NA
Aus	269	85.50%	2.20%	4.83%	7.43%	NA
Indica I	595	72.40%	5.20%	6.55%	15.80%	NA
Indica II	465	52.30%	26.70%	9.25%	11.83%	NA
Indica III	913	58.60%	15.40%	6.24%	19.72%	NA
Indica Intermediate	786	59.20%	20.10%	6.62%	14.12%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	92.70%	0.20%	1.98%	5.16%	NA
Japonica Intermediate	241	84.60%	2.10%	2.90%	10.37%	NA
VI/Aromatic	96	93.80%	0.00%	4.17%	2.08%	NA
Intermediate	90	86.70%	6.70%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108752863	G -> DEL	N	N	silent_mutation	Average:26.996; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg1108752863	G -> C	LOC_Os11g15450.1	upstream_gene_variant ; 3521.0bp to feature; MODIFIER	silent_mutation	Average:26.996; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg1108752863	G -> C	LOC_Os11g15440.1	intron_variant ; MODIFIER	silent_mutation	Average:26.996; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108752863	2.50E-06	2.11E-06	mr1748_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