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Detailed information for vg1121315763:

Variant ID: vg1121315763 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21315763
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAGCGCATCCTCCGTGCTGCCAACGCCGGAGGCTTCCCCCTCCTGAGGAACCACGAGCACGGGCTCGGCACGAGGGGTCTCCACGAAGCAGGTCCACGC[T/C]
AGGGACTGACGAATAAGCTCGGGCCTGGAGGTACTCTTGCGGGCGGTGATCTTCTGGCTACGGCAGACGCGGCGGCGCTTGGGACGGCAGACCTCTCCCT

Reverse complement sequence

AGGGAGAGGTCTGCCGTCCCAAGCGCCGCCGCGTCTGCCGTAGCCAGAAGATCACCGCCCGCAAGAGTACCTCCAGGCCCGAGCTTATTCGTCAGTCCCT[A/G]
GCGTGGACCTGCTTCGTGGAGACCCCTCGTGCCGAGCCCGTGCTCGTGGTTCCTCAGGAGGGGGAAGCCTCCGGCGTTGGCAGCACGGAGGATGCGCTGC

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	28.50%	26.30%	9.80%	35.42%	NA
All Indica	2759	36.00%	8.30%	11.02%	44.73%	NA
All Japonica	1512	11.90%	64.20%	2.71%	21.16%	NA
Aus	269	42.00%	5.60%	34.94%	17.47%	NA
Indica I	595	60.50%	23.50%	6.89%	9.08%	NA
Indica II	465	37.00%	5.80%	15.70%	41.51%	NA
Indica III	913	18.70%	1.30%	10.84%	69.11%	NA
Indica Intermediate	786	36.80%	6.40%	11.58%	45.29%	NA
Temperate Japonica	767	7.70%	78.60%	1.04%	12.65%	NA
Tropical Japonica	504	17.90%	52.40%	4.96%	24.80%	NA
Japonica Intermediate	241	12.90%	43.20%	3.32%	40.66%	NA
VI/Aromatic	96	35.40%	1.00%	15.62%	47.92%	NA
Intermediate	90	30.00%	30.00%	10.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121315763	T -> DEL	LOC_Os11g36220.1	N	frameshift_variant	Average:22.758; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg1121315763	T -> C	LOC_Os11g36220.1	synonymous_variant ; p.Leu249Leu; LOW	synonymous_codon	Average:22.758; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121315763	1.87E-06	1.87E-06	mr1361	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