RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0103252222:

Variant ID: vg0103252222 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3252222
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAACACTAGGTCTAGCAGCAACCAATTTATCTTATCACATACCGTCCTCATTTGCCAATCTCAAGTCCTTGAAGCGTTTGGGTATGAGCACGGCACGAA[C/T]
TTCCAAGGAGCTGCCCTCTTTATTAGATAAGCTTCCTTCATTGACAGAACTGGAATTGCAAGGATCGGAATCAGGCTTGGAGAAGGCGGTATTATCTTGG

Reverse complement sequence

CCAAGATAATACCGCCTTCTCCAAGCCTGATTCCGATCCTTGCAATTCCAGTTCTGTCAATGAAGGAAGCTTATCTAATAAAGAGGGCAGCTCCTTGGAA[G/A]
TTCGTGCCGTGCTCATACCCAAACGCTTCAAGGACTTGAGATTGGCAAATGAGGACGGTATGTGATAAGATAAATTGGTTGCTGCTAGACCTAGTGTTTC

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	61.60%	25.90%	0.06%	12.44%	NA
All Indica	2759	92.10%	5.90%	0.07%	1.85%	NA
All Japonica	1512	19.10%	46.00%	0.07%	34.79%	NA
Aus	269	9.70%	90.30%	0.00%	0.00%	NA
Indica I	595	97.80%	0.50%	0.17%	1.51%	NA
Indica II	465	92.50%	6.20%	0.00%	1.29%	NA
Indica III	913	87.30%	10.10%	0.11%	2.52%	NA
Indica Intermediate	786	93.30%	5.10%	0.00%	1.65%	NA
Temperate Japonica	767	19.00%	75.00%	0.13%	5.87%	NA
Tropical Japonica	504	18.70%	5.60%	0.00%	75.79%	NA
Japonica Intermediate	241	20.30%	38.60%	0.00%	41.08%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	56.70%	31.10%	0.00%	12.22%	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
vg0103252222	C -> T	LOC_Os01g06870.1	missense_variant ; p.Thr340Ile; MODERATE	nonsynonymous_codon ; T340I	Average:60.141; most accessible tissue: Zhenshan97 root, score: 82.912	unknown	unknown	TOLERATED	0.52
vg0103252222	C -> DEL	LOC_Os01g06870.1	N	frameshift_variant	Average:60.141; most accessible tissue: Zhenshan97 root, score: 82.912	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
vg0103252222	NA	3.21E-09	mr1047	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
vg0103252222	NA	9.20E-11	mr1151	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
vg0103252222	NA	1.09E-18	mr1164	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
vg0103252222	NA	7.15E-08	mr1174	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
vg0103252222	NA	8.93E-13	mr1183	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
vg0103252222	NA	4.14E-06	mr1189	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
vg0103252222	9.02E-06	2.23E-12	mr1205	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
vg0103252222	NA	2.42E-06	mr1215	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
vg0103252222	NA	9.18E-10	mr1249	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
vg0103252222	3.53E-06	NA	mr1328	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

Showing 1 to 10 of 23 entries

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Search for Variation information by Variation ID:

Detailed information for vg0103252222:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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