RiceVarMap2

Detailed information for vg0507097189:

Variant ID: vg0507097189 (JBrowse)

Variation Type: SNP

Chromosome: chr05

Position: 7097189

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGTTGTCGGCGTCGGAGTCCGACGAAGCAGGGACCCTTCGCTTCCTAGGGGCAAGCTTCACTTGCCCGCGCATTCGCTTTCGCGAAGGCCCTGCATCGT[C/T]
GTCCGCTTTGTGGGGGTTTGCCCGAGGAGGCAACTCGCTGTTATAAACCCGGTTCGCCCGCCCAGACGCTTGTCGTTAGGGATGACAACAGAGCGGATAC

Reverse complement sequence

GTATCCGCTCTGTTGTCATCCCTAACGACAAGCGTCTGGGCGGGCGAACCGGGTTTATAACAGCGAGTTGCCTCCTCGGGCAAACCCCCACAAAGCGGAC[G/A]
ACGATGCAGGGCCTTCGCGAAAGCGAATGCGCGGGCAAGTGAAGCTTGCCCCTAGGAAGCGAAGGGTCCCTGCTTCGTCGGACTCCGACGCCGACAACGA

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	60.90%	3.40%	1.48%	34.17%	NA
All Indica	2759	59.10%	5.90%	1.96%	33.09%	NA
All Japonica	1512	63.10%	0.00%	0.40%	36.51%	NA
Aus	269	87.40%	0.00%	2.23%	10.41%	NA
Indica I	595	73.60%	10.80%	1.01%	14.62%	NA
Indica II	465	33.80%	1.30%	3.87%	61.08%	NA
Indica III	913	56.60%	5.40%	1.86%	36.14%	NA
Indica Intermediate	786	65.90%	5.50%	1.65%	26.97%	NA
Temperate Japonica	767	91.90%	0.00%	0.26%	7.82%	NA
Tropical Japonica	504	20.20%	0.00%	0.60%	79.17%	NA
Japonica Intermediate	241	61.00%	0.00%	0.41%	38.59%	NA
VI/Aromatic	96	9.40%	0.00%	2.08%	88.54%	NA
Intermediate	90	56.70%	0.00%	2.22%	41.11%	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
vg0507097189	C -> T	LOC_Os05g12350.1	missense_variant ; p.Asp253Asn; MODERATE	nonsynonymous_codon ; D253N	Average:31.945; most accessible tissue: Minghui63 panicle, score: 42.799	benign	0.754	TOLERATED	0.08
vg0507097189	C -> DEL	LOC_Os05g12350.1	N	frameshift_variant	Average:31.945; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507097189	8.80E-07	2.68E-07	mr1496_2	Ind_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

Contact

Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China

Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/

Search for Variation information by Variation ID:

Detailed information for vg0507097189:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

RiceVarMap v2.0

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