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Detailed information for vg1100554526:

Variant ID: vg1100554526 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 554526
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.12, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CCTAGTCTATGATGCCCGCAGACATCCCGAATCACACAGATTCGTTTCTGACCACTCAGGTCATCCATCTGCCACATAGGCTGATTCTGGTTACGATTCC[C/T]
ATACCACAACACTTTTCATAAAGCACAGGCAAACAAATCTACGCAACGGGAAACACCTCACATCCGCCCATGACCGTGGGCATGGCTGTTCGAACAGTTG

Reverse complement sequence

CAACTGTTCGAACAGCCATGCCCACGGTCATGGGCGGATGTGAGGTGTTTCCCGTTGCGTAGATTTGTTTGCCTGTGCTTTATGAAAAGTGTTGTGGTAT[G/A]
GGAATCGTAACCAGAATCAGCCTATGTGGCAGATGGATGACCTGAGTGGTCAGAAACGAATCTGTGTGATTCGGGATGTCTGCGGGCATCATAGACTAGG

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	80.80%	19.00%	0.11%	0.06%	NA
All Indica	2759	74.70%	25.10%	0.18%	0.07%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	27.90%	71.70%	0.00%	0.37%	NA
Indica I	595	70.90%	28.60%	0.50%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	67.00%	32.70%	0.00%	0.22%	NA
Indica Intermediate	786	74.30%	25.40%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1100554526	C -> T	LOC_Os11g02070.1	downstream_gene_variant ; 4267.0bp to feature; MODIFIER	silent_mutation	Average:54.16; most accessible tissue: Zhenshan97 root, score: 83.426	N	N	N	N
vg1100554526	C -> T	LOC_Os11g02054.1	intron_variant ; MODIFIER	silent_mutation	Average:54.16; most accessible tissue: Zhenshan97 root, score: 83.426	N	N	N	N
vg1100554526	C -> DEL	N	N	silent_mutation	Average:54.16; most accessible tissue: Zhenshan97 root, score: 83.426	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1100554526	3.80E-07	NA	mr1095	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