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Detailed information for vg1118086655:

Variant ID: vg1118086655 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18086655
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACAAAGTTTGCATGTAAATCGTGAGACGAATCTTTTAAGTCTAATTAGGTCATGATTAGCCATAAGTTCTATAGTAACCCATATGTGCTAATGACGGAT[T/C]
AATTAGGCTCAAAAGATTTGTCTCGCAGTTTCCAGGCGAGTTATGAAATTAGTTTTTTTATTCGTGTCCAAAAACCCCTTCCGATATCCGGTCAAACGTC

Reverse complement sequence

GACGTTTGACCGGATATCGGAAGGGGTTTTTGGACACGAATAAAAAAACTAATTTCATAACTCGCCTGGAAACTGCGAGACAAATCTTTTGAGCCTAATT[A/G]
ATCCGTCATTAGCACATATGGGTTACTATAGAACTTATGGCTAATCATGACCTAATTAGACTTAAAAGATTCGTCTCACGATTTACATGCAAACTTTGTA

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	34.90%	0.40%	0.66%	64.11%	NA
All Indica	2759	16.90%	0.30%	0.62%	82.13%	NA
All Japonica	1512	69.60%	0.40%	0.86%	29.17%	NA
Aus	269	21.60%	0.00%	0.00%	78.44%	NA
Indica I	595	24.40%	0.30%	0.67%	74.62%	NA
Indica II	465	30.10%	0.20%	1.29%	68.39%	NA
Indica III	913	4.30%	0.50%	0.11%	95.07%	NA
Indica Intermediate	786	18.20%	0.10%	0.76%	80.92%	NA
Temperate Japonica	767	94.40%	0.10%	1.04%	4.43%	NA
Tropical Japonica	504	47.60%	0.40%	0.60%	51.39%	NA
Japonica Intermediate	241	36.50%	1.20%	0.83%	61.41%	NA
VI/Aromatic	96	35.40%	2.10%	1.04%	61.46%	NA
Intermediate	90	41.10%	0.00%	0.00%	58.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1118086655	T -> DEL	N	N	silent_mutation	Average:41.735; most accessible tissue: Minghui63 panicle, score: 87.951	N	N	N	N
vg1118086655	T -> C	LOC_Os11g31080.1	downstream_gene_variant ; 2378.0bp to feature; MODIFIER	silent_mutation	Average:41.735; most accessible tissue: Minghui63 panicle, score: 87.951	N	N	N	N
vg1118086655	T -> C	LOC_Os11g31070-LOC_Os11g31080	intergenic_region ; MODIFIER	silent_mutation	Average:41.735; most accessible tissue: Minghui63 panicle, score: 87.951	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118086655	4.66E-06	4.66E-06	mr1300	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
vg1118086655	2.46E-06	2.46E-06	mr1926	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