RiceVarMap2

Detailed information for vg0136519161:

Variant ID: vg0136519161 (JBrowse)

Variation Type: SNP

Chromosome: chr01

Position: 36519161

Reference Allele: G

Alternative Allele: A

Primary Allele: G

Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTGTGGAGTAGTTTGTGGGTGTGTGGTATCCCATGGCAGTTGTGTCTCCCCATGGATGGAGAGGACCTTGTATATCCTCAATGGTATCAATAACTTTC[G/A]
TTACTGCTGCCCTTATCGCTATCTTAACTGCCGTTGTAATATTAGTCTTGAAAGCTCTCTTGAATAGGTTAGATGCGTGAATAGCAGTTTGCATGGTGCT

Reverse complement sequence

AGCACCATGCAAACTGCTATTCACGCATCTAACCTATTCAAGAGAGCTTTCAAGACTAATATTACAACGGCAGTTAAGATAGCGATAAGGGCAGCAGTAA[C/T]
GAAAGTTATTGATACCATTGAGGATATACAAGGTCCTCTCCATCCATGGGGAGACACAACTGCCATGGGATACCACACACCCACAAACTACTCCACACAT

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	36.00%	0.80%	6.01%	57.28%	NA
All Indica	2759	4.10%	0.00%	5.73%	90.14%	NA
All Japonica	1512	94.60%	2.40%	0.40%	2.65%	NA
Aus	269	1.90%	0.00%	42.38%	55.76%	NA
Indica I	595	2.50%	0.00%	3.87%	93.61%	NA
Indica II	465	4.50%	0.00%	3.66%	91.83%	NA
Indica III	913	2.60%	0.00%	6.90%	90.47%	NA
Indica Intermediate	786	6.90%	0.00%	7.00%	86.13%	NA
Temperate Japonica	767	98.80%	0.00%	0.00%	1.17%	NA
Tropical Japonica	504	88.70%	7.10%	1.19%	2.98%	NA
Japonica Intermediate	241	93.40%	0.00%	0.00%	6.64%	NA
VI/Aromatic	96	92.70%	0.00%	1.04%	6.25%	NA
Intermediate	90	67.80%	0.00%	5.56%	26.67%	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
vg0136519161	G -> A	LOC_Os01g63040.1	missense_variant ; p.Thr487Met; MODERATE	nonsynonymous_codon ; T487M	Average:4.671; most accessible tissue: Minghui63 panicle, score: 7.125	unknown	unknown	TOLERATED	0.06
vg0136519161	G -> DEL	LOC_Os01g63040.1	N	frameshift_variant	Average:4.671; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Showing 1 to 2 of 2 entries

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 vg0136519161:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

Tools

Blast

Design Primer by Variation ID

Design Primer by Region

Haplotype Network Analysis

Varitation Coordinate Convert

Contact