RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0413262397:

Variant ID: vg0413262397 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13262397
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGTTTTTTGGGCAACCCCCTTTCACGGTGACGATTGACCTTAGCATCCTCCTATCAAATGAAGACACCCCTTACTCACGTAGCGATCACAAGGAAGGAA[C/T]
AATAGTGAGGAGAAAGTACGTGCGGTCAACCGTCACCGCCGATGTATTGCCGTAATTGTTGTGTACACGATTTATTGAATATCGATATGAATCAATTGTT

Reverse complement sequence

AACAATTGATTCATATCGATATTCAATAAATCGTGTACACAACAATTACGGCAATACATCGGCGGTGACGGTTGACCGCACGTACTTTCTCCTCACTATT[G/A]
TTCCTTCCTTGTGATCGCTACGTGAGTAAGGGGTGTCTTCATTTGATAGGAGGATGCTAAGGTCAATCGTCACCGTGAAAGGGGGTTGCCCAAAAAACTG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.00%	21.90%	0.06%	0.00%	NA
All Indica	2759	90.10%	9.90%	0.00%	0.00%	NA
All Japonica	1512	65.30%	34.50%	0.20%	0.00%	NA
Aus	269	22.70%	77.30%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.30%	4.70%	0.00%	0.00%	NA
Indica III	913	82.60%	17.40%	0.00%	0.00%	NA
Indica Intermediate	786	88.40%	11.60%	0.00%	0.00%	NA
Temperate Japonica	767	89.20%	10.60%	0.26%	0.00%	NA
Tropical Japonica	504	24.60%	75.40%	0.00%	0.00%	NA
Japonica Intermediate	241	74.70%	24.90%	0.41%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	0.00%	0.00%	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
vg0413262397	C -> T	LOC_Os04g23240.1	missense_variant ; p.Thr818Ile; MODERATE	nonsynonymous_codon ; T818I	Average:15.596; most accessible tissue: Minghui63 panicle, score: 29.741	probably damaging	2.188	DELETERIOUS	0.00

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413262397	NA	5.42E-09	mr1029	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
vg0413262397	4.61E-06	5.37E-08	mr1029	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
vg0413262397	NA	7.84E-10	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
vg0413262397	NA	6.41E-08	mr1047	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
vg0413262397	NA	1.48E-08	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
vg0413262397	1.34E-08	1.34E-08	mr1189	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
vg0413262397	NA	8.88E-08	mr1471	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
vg0413262397	NA	2.53E-08	mr1625	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
vg0413262397	8.52E-06	1.97E-07	mr1625	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
vg0413262397	NA	8.01E-08	mr1642	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 19 entries

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Search for Variation information by Variation ID:

Detailed information for vg0413262397:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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