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Detailed information for vg1127933245:

Variant ID: vg1127933245 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27933245
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAGACGCAACTAGATGGTTACAAGGGGACATGATATAACAATTAACAAAGGGAGGATCAATGCAACAAACTAGGTAGGTCCGCCAATCTGCCTTGCAGA[T/C]
GGGACAAACAGATTAAGTACGGTCCTATTAATGCATAATATTTTTCAAGCAACATAATTAAATTTCAATTATAGGCTCAAGATGTTCAAAGGTGGCTTGC

Reverse complement sequence

GCAAGCCACCTTTGAACATCTTGAGCCTATAATTGAAATTTAATTATGTTGCTTGAAAAATATTATGCATTAATAGGACCGTACTTAATCTGTTTGTCCC[A/G]
TCTGCAAGGCAGATTGGCGGACCTACCTAGTTTGTTGCATTGATCCTCCCTTTGTTAATTGTTATATCATGTCCCCTTGTAACCATCTAGTTGCGTCTCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.00%	4.10%	11.96%	14.96%	NA
All Indica	2759	79.40%	0.90%	13.48%	6.20%	NA
All Japonica	1512	48.50%	7.10%	10.32%	34.13%	NA
Aus	269	70.30%	21.60%	6.69%	1.49%	NA
Indica I	595	71.80%	0.00%	13.78%	14.45%	NA
Indica II	465	72.70%	0.60%	20.22%	6.45%	NA
Indica III	913	86.20%	1.10%	12.16%	0.55%	NA
Indica Intermediate	786	81.20%	1.70%	10.81%	6.36%	NA
Temperate Japonica	767	42.80%	1.40%	12.65%	43.16%	NA
Tropical Japonica	504	61.10%	6.50%	6.75%	25.60%	NA
Japonica Intermediate	241	40.20%	26.10%	10.37%	23.24%	NA
VI/Aromatic	96	76.00%	0.00%	15.62%	8.33%	NA
Intermediate	90	83.30%	3.30%	4.44%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127933245	T -> DEL	N	N	silent_mutation	Average:16.561; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1127933245	T -> C	LOC_Os11g46140.1	downstream_gene_variant ; 2200.0bp to feature; MODIFIER	silent_mutation	Average:16.561; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1127933245	T -> C	LOC_Os11g46140-LOC_Os11g46150	intergenic_region ; MODIFIER	silent_mutation	Average:16.561; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127933245	1.12E-06	3.11E-07	mr1289_2	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