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Detailed information for vg1121410763:

Variant ID: vg1121410763 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21410763
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCGGCGATCTTCTCCAACTGACCGAGAAAATGAACTAAAATGATACTCCCTCCTTACCTAAATGGACACCGTTGATTTTTTTAAACATATTTGACCGTT[T/C]
GTCTTATTCAAAAACTTTTATGAAATATGTAAAACTATATGTATAGATAAAAGTATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATAATTACT

Reverse complement sequence

AGTAATTATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATACTTTTATCTATACATATAGTTTTACATATTTCATAAAAGTTTTTGAATAAGAC[A/G]
AACGGTCAAATATGTTTAAAAAAATCAACGGTGTCCATTTAGGTAAGGAGGGAGTATCATTTTAGTTCATTTTCTCGGTCAGTTGGAGAAGATCGCCGGT

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	68.70%	22.20%	3.05%	5.99%	NA
All Indica	2759	79.80%	5.50%	4.93%	9.79%	NA
All Japonica	1512	45.80%	53.10%	0.40%	0.73%	NA
Aus	269	90.00%	9.70%	0.37%	0.00%	NA
Indica I	595	68.10%	18.20%	7.06%	6.72%	NA
Indica II	465	71.80%	0.60%	9.25%	18.28%	NA
Indica III	913	91.30%	0.80%	0.99%	6.90%	NA
Indica Intermediate	786	79.90%	4.30%	5.34%	10.43%	NA
Temperate Japonica	767	31.70%	67.00%	0.26%	1.04%	NA
Tropical Japonica	504	55.60%	43.70%	0.20%	0.60%	NA
Japonica Intermediate	241	70.10%	28.60%	1.24%	0.00%	NA
VI/Aromatic	96	57.30%	42.70%	0.00%	0.00%	NA
Intermediate	90	65.60%	31.10%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121410763	T -> DEL	N	N	silent_mutation	Average:49.489; most accessible tissue: Zhenshan97 root, score: 71.174	N	N	N	N
vg1121410763	T -> C	LOC_Os11g36340.1	upstream_gene_variant ; 2833.0bp to feature; MODIFIER	silent_mutation	Average:49.489; most accessible tissue: Zhenshan97 root, score: 71.174	N	N	N	N
vg1121410763	T -> C	LOC_Os11g36330.1	downstream_gene_variant ; 4391.0bp to feature; MODIFIER	silent_mutation	Average:49.489; most accessible tissue: Zhenshan97 root, score: 71.174	N	N	N	N
vg1121410763	T -> C	LOC_Os11g36330-LOC_Os11g36340	intergenic_region ; MODIFIER	silent_mutation	Average:49.489; most accessible tissue: Zhenshan97 root, score: 71.174	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121410763	4.67E-06	NA	mr1718_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