RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0137169061:

Variant ID: vg0137169061 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 37169061
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTGAGAAAATTTTTCCATGAATTATTTTGGTCTGAAGGAGTACTGGGCTTATATCAGTTAGTCATACATTGACAAGAAGAAATAATTTGAGAGAATTCA[A/G]
TTAAAGTTAATCAAGCTGAAATTAAGTTATAAAGATAATCATTTATGATTCAGCTGACAGAAGCTTGAGATTGGCTCAAATCTGGATGCATATAGATTTG

Reverse complement sequence

CAAATCTATATGCATCCAGATTTGAGCCAATCTCAAGCTTCTGTCAGCTGAATCATAAATGATTATCTTTATAACTTAATTTCAGCTTGATTAACTTTAA[T/C]
TGAATTCTCTCAAATTATTTCTTCTTGTCAATGTATGACTAACTGATATAAGCCCAGTACTCCTTCAGACCAAAATAATTCATGGAAAAATTTTCTCAGT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.80%	30.70%	0.59%	3.91%	NA
All Indica	2759	98.60%	1.40%	0.00%	0.04%	NA
All Japonica	1512	2.20%	84.20%	1.79%	11.77%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.60%	0.00%	0.22%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	96.20%	3.80%	0.00%	0.00%	NA
Temperate Japonica	767	1.70%	72.90%	3.39%	22.03%	NA
Tropical Japonica	504	3.00%	97.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	93.40%	0.41%	3.73%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	44.40%	47.80%	1.11%	6.67%	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
vg0137169061	A -> G	LOC_Os01g63990-LOC_Os01g64000	intergenic_region ; MODIFIER	silent_mutation	Average:24.826; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0137169061	A -> DEL	N	N	silent_mutation	Average:24.826; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0137169061	NA	3.23E-111	mr1008	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
vg0137169061	NA	2.81E-109	mr1009	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
vg0137169061	NA	1.35E-71	mr1014	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
vg0137169061	NA	5.20E-77	mr1015	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
vg0137169061	NA	5.35E-26	mr1024	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
vg0137169061	NA	8.69E-68	mr1027	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
vg0137169061	NA	1.11E-10	mr1128	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
vg0137169061	5.63E-07	1.42E-96	mr1134	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
vg0137169061	6.65E-10	2.39E-96	mr1135	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
vg0137169061	NA	5.50E-06	mr1135	Jap_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 10 of 66 entries

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Search for Variation information by Variation ID:

Detailed information for vg0137169061:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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