RiceVarMap2

Detailed information for vg1127723968:

Variant ID: vg1127723968 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 27723968

Reference Allele: A

Alternative Allele: G

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.57, A: 0.43, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCTGCTCAAATGTCCCCGTCGTCTATTCTGAACAGAACTTGTGGAATGGGTGGATGGGCATAAAGACAATGATTTTGACCAAACGCAGAGGGGAAAAT[A/G]
TCGGACTTTGGAAGCTGGAAATGATCCCCAACTCTGACCGCTCGGAGAGCCCGCTCATCCTAACCTGATCTGATGCCTTCAGCTTCTAGGTTCAGTAATC

Reverse complement sequence

GATTACTGAACCTAGAAGCTGAAGGCATCAGATCAGGTTAGGATGAGCGGGCTCTCCGAGCGGTCAGAGTTGGGGATCATTTCCAGCTTCCAAAGTCCGA[T/C]
ATTTTCCCCTCTGCGTTTGGTCAAAATCATTGTCTTTATGCCCATCCACCCATTCCACAAGTTCTGTTCAGAATAGACGACGGGGACATTTGAGCAGCTG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.50%	28.80%	0.59%	28.10%	NA
All Indica	2759	47.00%	25.30%	0.65%	27.04%	NA
All Japonica	1512	41.00%	38.00%	0.33%	20.70%	NA
Aus	269	14.90%	13.80%	1.49%	69.89%	NA
Indica I	595	37.80%	22.50%	1.85%	37.82%	NA
Indica II	465	43.40%	24.30%	0.22%	32.04%	NA
Indica III	913	58.40%	27.60%	0.55%	13.47%	NA
Indica Intermediate	786	43.00%	25.20%	0.13%	31.68%	NA
Temperate Japonica	767	37.80%	44.10%	0.26%	17.86%	NA
Tropical Japonica	504	48.60%	22.60%	0.60%	28.17%	NA
Japonica Intermediate	241	35.30%	50.60%	0.00%	14.11%	NA
VI/Aromatic	96	6.20%	28.10%	0.00%	65.62%	NA
Intermediate	90	47.80%	31.10%	1.11%	20.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127723968	A -> DEL	N	N	silent_mutation	Average:43.749; most accessible tissue: Callus, score: 95.085	N	N	N	N
vg1127723968	A -> G	LOC_Os11g45820.1	5_prime_UTR_premature_start_codon_gain_variant ; LOW	silent_mutation	Average:43.749; most accessible tissue: Callus, score: 95.085	N	N	N	N
vg1127723968	A -> G	LOC_Os11g45820.1	5_prime_UTR_variant ; 276.0bp to feature; MODIFIER	silent_mutation	Average:43.749; most accessible tissue: Callus, score: 95.085	N	N	N	N
vg1127723968	A -> G	LOC_Os11g45809.1	downstream_gene_variant ; 2868.0bp to feature; MODIFIER	silent_mutation	Average:43.749; most accessible tissue: Callus, score: 95.085	N	N	N	N

Showing 1 to 4 of 4 entries

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127723968	NA	6.74E-06	mr1191_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

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Detailed information for vg1127723968:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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