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Detailed information for vg1121955520:

Variant ID: vg1121955520 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21955520
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTGCTTTCAGGTTGAGCTGCACCGGTTTCGATCTTCAACAAGAGGTAAAACTCGTCGTGGCGAATTATGTTCTTAGGGATTAGTGCTTCCATCTTCAT[G/T]
ACATTCTAATCTCGTTTATATAATTCGCCGAGTTATCATATATCTTATATAATCTCTAGCAATATCGCTATCTAACCCACAATCGGCTAACATCTATTAA

Reverse complement sequence

TTAATAGATGTTAGCCGATTGTGGGTTAGATAGCGATATTGCTAGAGATTATATAAGATATATGATAACTCGGCGAATTATATAAACGAGATTAGAATGT[C/A]
ATGAAGATGGAAGCACTAATCCCTAAGAACATAATTCGCCACGACGAGTTTTACCTCTTGTTGAAGATCGAAACCGGTGCAGCTCAACCTGAAAGCAAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.20%	1.30%	7.26%	12.29%	NA
All Indica	2759	71.80%	1.90%	11.49%	14.75%	NA
All Japonica	1512	93.00%	0.50%	1.19%	5.29%	NA
Aus	269	75.10%	0.00%	0.74%	24.16%	NA
Indica I	595	89.20%	0.80%	6.05%	3.87%	NA
Indica II	465	67.50%	0.90%	13.98%	17.63%	NA
Indica III	913	66.50%	3.50%	13.03%	16.98%	NA
Indica Intermediate	786	67.40%	1.50%	12.34%	18.70%	NA
Temperate Japonica	767	96.50%	0.10%	1.43%	1.96%	NA
Tropical Japonica	504	86.70%	1.20%	1.19%	10.91%	NA
Japonica Intermediate	241	95.00%	0.40%	0.41%	4.15%	NA
VI/Aromatic	96	79.20%	0.00%	2.08%	18.75%	NA
Intermediate	90	83.30%	0.00%	4.44%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121955520	G -> T	LOC_Os11g37180.1	upstream_gene_variant ; 859.0bp to feature; MODIFIER	silent_mutation	Average:23.028; most accessible tissue: Callus, score: 36.579	N	N	N	N
vg1121955520	G -> T	LOC_Os11g37170.1	downstream_gene_variant ; 4500.0bp to feature; MODIFIER	silent_mutation	Average:23.028; most accessible tissue: Callus, score: 36.579	N	N	N	N
vg1121955520	G -> T	LOC_Os11g37180-LOC_Os11g37190	intergenic_region ; MODIFIER	silent_mutation	Average:23.028; most accessible tissue: Callus, score: 36.579	N	N	N	N
vg1121955520	G -> DEL	N	N	silent_mutation	Average:23.028; most accessible tissue: Callus, score: 36.579	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121955520	1.56E-06	3.61E-07	mr1018	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