RiceVarMap2

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Detailed information for vg0139341179:

Variant ID: vg0139341179 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39341179
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCGAGTTTCTCTGAAACCGAGTGGCCTTGGAGGAGATTGGCGGCTGCCGTGCCTGAGGAAGACGACGACGACGCCATGTGGATGAAAGATGCGATCTA[T/C]
CGAGGTGGAAAAAGGATCTGATACCATGTGATAAAATGTGAAGCGTTGAACCCTTTGCCTCGGGCCGCATCTCTGTTAAATAGTGGTAGAAACAGCCTCT

Reverse complement sequence

AGAGGCTGTTTCTACCACTATTTAACAGAGATGCGGCCCGAGGCAAAGGGTTCAACGCTTCACATTTTATCACATGGTATCAGATCCTTTTTCCACCTCG[A/G]
TAGATCGCATCTTTCATCCACATGGCGTCGTCGTCGTCTTCCTCAGGCACGGCAGCCGCCAATCTCCTCCAAGGCCACTCGGTTTCAGAGAAACTCGGGA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.30%	26.20%	7.64%	31.93%	NA
All Indica	2759	4.30%	33.60%	12.11%	49.91%	NA
All Japonica	1512	93.30%	2.10%	0.93%	3.77%	NA
Aus	269	3.00%	93.70%	1.12%	2.23%	NA
Indica I	595	4.00%	30.10%	18.15%	47.73%	NA
Indica II	465	4.70%	4.10%	9.46%	81.72%	NA
Indica III	913	2.20%	50.90%	9.64%	37.24%	NA
Indica Intermediate	786	6.90%	33.70%	11.96%	47.46%	NA
Temperate Japonica	767	98.70%	0.10%	0.13%	1.04%	NA
Tropical Japonica	504	85.90%	5.40%	1.79%	6.94%	NA
Japonica Intermediate	241	91.30%	1.20%	1.66%	5.81%	NA
VI/Aromatic	96	33.30%	13.50%	4.17%	48.96%	NA
Intermediate	90	54.40%	14.40%	6.67%	24.44%	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
vg0139341179	T -> DEL	N	N	silent_mutation	Average:8.964; most accessible tissue: Callus, score: 42.343	N	N	N	N
vg0139341179	T -> C	LOC_Os01g67690.1	upstream_gene_variant ; 22.0bp to feature; MODIFIER	silent_mutation	Average:8.964; most accessible tissue: Callus, score: 42.343	N	N	N	N
vg0139341179	T -> C	LOC_Os01g67700.1	upstream_gene_variant ; 4254.0bp to feature; MODIFIER	silent_mutation	Average:8.964; most accessible tissue: Callus, score: 42.343	N	N	N	N
vg0139341179	T -> C	LOC_Os01g67690-LOC_Os01g67700	intergenic_region ; MODIFIER	silent_mutation	Average:8.964; most accessible tissue: Callus, score: 42.343	N	N	N	N

Showing 1 to 4 of 4 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0139341179	NA	2.92E-10	Grain_weight	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0139341179	6.47E-06	8.49E-06	mr1453	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
vg0139341179	NA	2.19E-18	mr1383_2	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

Showing 1 to 3 of 3 entries

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Search for Variation information by Variation ID:

Detailed information for vg0139341179:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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