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Detailed information for vg1102590535:

Variant ID: vg1102590535 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 2590535
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAATTAAAGCAATGTCACGAAAATATTGAAAGTTTGTGTGTAGAATAATTTTTATGTGATGGAAAAGTTGGAAGTTTAAAGAAAAAGTTTGGAACTAAA[C/T]
TCGGCCCTGGTTGACAGCAAACTTTTAAAAATATAGTGAAGTTGAATTTTTCACCTTTTAATTTCTAGCTACGCCGTGTTTAGTTTCAAAATAATTCTTC

Reverse complement sequence

GAAGAATTATTTTGAAACTAAACACGGCGTAGCTAGAAATTAAAAGGTGAAAAATTCAACTTCACTATATTTTTAAAAGTTTGCTGTCAACCAGGGCCGA[G/A]
TTTAGTTCCAAACTTTTTCTTTAAACTTCCAACTTTTCCATCACATAAAAATTATTCTACACACAAACTTTCAATATTTTCGTGACATTGCTTTAATTTC

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	56.00%	6.60%	9.94%	27.47%	NA
All Indica	2759	29.20%	11.10%	15.66%	44.00%	NA
All Japonica	1512	99.20%	0.20%	0.00%	0.60%	NA
Aus	269	65.80%	0.40%	11.15%	22.68%	NA
Indica I	595	67.40%	14.30%	7.90%	10.42%	NA
Indica II	465	9.50%	8.00%	6.45%	76.13%	NA
Indica III	913	12.30%	6.90%	26.62%	54.22%	NA
Indica Intermediate	786	31.80%	15.40%	14.25%	38.55%	NA
Temperate Japonica	767	99.00%	0.30%	0.00%	0.78%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	74.40%	2.20%	7.78%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1102590535	C -> T	LOC_Os11g05680-LOC_Os11g05690	intergenic_region ; MODIFIER	silent_mutation	Average:46.714; most accessible tissue: Callus, score: 90.843	N	N	N	N
vg1102590535	C -> DEL	N	N	silent_mutation	Average:46.714; most accessible tissue: Callus, score: 90.843	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1102590535	4.52E-10	3.69E-12	mr1397	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