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Detailed information for vg1112979407:

Variant ID: vg1112979407 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12979407
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCATGTAGAGTTCTGCTAGTTTCTTTCCATCAAAGGTGGTTTTCACTGGCACGAAATGAGCTGATTTCATGAGTCAATCCACGATTATCCAGATGGAGT[C/T,A]
GTACCCACTAGGGGTTCTTGGCAAACCGGTGATGAAATCCATTCTATCTCTTCCCATTTGCACTCGGGAATCGATAGGGGTTGCAGCAGACCAGCTGGCC

Reverse complement sequence

GGCCAGCTGGTCTGCTGCAACCCCTATCGATTCCCGAGTGCAAATGGGAAGAGATAGAATGGATTTCATCACCGGTTTGCCAAGAACCCCTAGTGGGTAC[G/A,T]
ACTCCATCTGGATAATCGTGGATTGACTCATGAAATCAGCTCATTTCGTGCCAGTGAAAACCACCTTTGATGGAAAGAAACTAGCAGAACTCTACATGAC

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	64.20%	0.50%	25.58%	9.71%	A: 0.02%
All Indica	2759	41.60%	0.80%	42.12%	15.37%	A: 0.04%
All Japonica	1512	98.10%	0.00%	0.79%	1.06%	NA
Aus	269	89.20%	0.40%	6.69%	3.72%	NA
Indica I	595	63.00%	0.80%	23.03%	13.11%	NA
Indica II	465	36.80%	1.90%	38.06%	23.23%	NA
Indica III	913	28.10%	0.30%	59.04%	12.38%	A: 0.11%
Indica Intermediate	786	44.00%	0.80%	39.31%	15.90%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	95.80%	0.00%	2.18%	1.98%	NA
Japonica Intermediate	241	97.90%	0.00%	0.41%	1.66%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	72.20%	1.10%	16.67%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112979407	C -> T	LOC_Os11g22570.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:10.414; most accessible tissue: Callus, score: 23.217	N	N	N	N
vg1112979407	C -> A	LOC_Os11g22570.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:10.414; most accessible tissue: Callus, score: 23.217	N	N	N	N
vg1112979407	C -> DEL	N	N	silent_mutation	Average:10.414; most accessible tissue: Callus, score: 23.217	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112979407	2.97E-06	2.97E-06	mr1508	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
vg1112979407	NA	6.04E-12	mr1657	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
vg1112979407	NA	7.39E-14	mr1325_2	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
vg1112979407	NA	2.26E-08	mr1690_2	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
vg1112979407	3.62E-06	NA	mr1758_2	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