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Detailed information for vg1103989226:

Variant ID: vg1103989226 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 3989226
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAGGCCATTCACCGAGCTTCTTGTTTGCATTCAGCCTATGTGTGACACGTTGGAGATTTGGTACCACATCCATCTCTGGCGCTACCCACCTGAAGCCCA[C/T]
GCGTCCAAATAAGGGCACTTATTTTTCAGCTAACATTGTCAAAAAAAGCAAGGGAGATGAGCCTTGGGAAGCGGGTACAATGGATCCGAAGTTGCCGCTC

Reverse complement sequence

GAGCGGCAACTTCGGATCCATTGTACCCGCTTCCCAAGGCTCATCTCCCTTGCTTTTTTTGACAATGTTAGCTGAAAAATAAGTGCCCTTATTTGGACGC[G/A]
TGGGCTTCAGGTGGGTAGCGCCAGAGATGGATGTGGTACCAAATCTCCAACGTGTCACACATAGGCTGAATGCAAACAAGAAGCTCGGTGAATGGCCTAA

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	94.80%	1.40%	1.21%	2.64%	NA
All Indica	2759	95.80%	0.20%	0.18%	3.81%	NA
All Japonica	1512	91.90%	3.70%	3.37%	0.99%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	88.80%	0.00%	0.44%	10.73%	NA
Indica Intermediate	786	98.30%	0.60%	0.13%	0.89%	NA
Temperate Japonica	767	96.60%	1.20%	2.22%	0.00%	NA
Tropical Japonica	504	85.70%	7.30%	4.76%	2.18%	NA
Japonica Intermediate	241	90.00%	4.10%	4.15%	1.66%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	95.60%	2.20%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1103989226	C -> T	LOC_Os11g07800.1	upstream_gene_variant ; 4017.0bp to feature; MODIFIER	silent_mutation	Average:70.577; most accessible tissue: Minghui63 root, score: 82.967	N	N	N	N
vg1103989226	C -> T	LOC_Os11g07820.1	upstream_gene_variant ; 250.0bp to feature; MODIFIER	silent_mutation	Average:70.577; most accessible tissue: Minghui63 root, score: 82.967	N	N	N	N
vg1103989226	C -> T	LOC_Os11g07810.1	downstream_gene_variant ; 532.0bp to feature; MODIFIER	silent_mutation	Average:70.577; most accessible tissue: Minghui63 root, score: 82.967	N	N	N	N
vg1103989226	C -> T	LOC_Os11g07810-LOC_Os11g07820	intergenic_region ; MODIFIER	silent_mutation	Average:70.577; most accessible tissue: Minghui63 root, score: 82.967	N	N	N	N
vg1103989226	C -> DEL	N	N	silent_mutation	Average:70.577; most accessible tissue: Minghui63 root, score: 82.967	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1103989226	4.30E-07	2.94E-10	mr1676_2	Jap_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