RiceVarMap2

Search for Variation information by Variation ID:

Flanking Sequence (100 bp) in Reference Genome:

TTTCCAACCAATTCACAAAGCAACTATCGAATTACCACATTTATTTTCATATTCTTACTCACCTCTAAACCTTATTTACCAAACACATTGATGACACAGT[AAA/AA,AAAA]
AAAAAATGCATTCATGGCAAATTGGACTAGTAAGCAAATACTCTTCACATCGCACCAGTAAATTTTTCTCACCCTAAATTACAATATCAGCAGTAAAGAA

Reverse complement sequence

TTCTTTACTGCTGATATTGTAATTTAGGGTGAGAAAAATTTACTGGTGCGATGTGAAGAGTATTTGCTTACTAGTCCAATTTGCCATGAATGCATTTTTT[TTT/TT,TTTT]
ACTGTGTCATCAATGTGTTTGGTAAATAAGGTTTAGAGGTGAGTAAGAATATGAAAATAAATGTGGTAATTCGATAGTTGCTTTGTGAATTGGTTGGAAA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of AAA(primary allele)	Frequency of AAAA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	774	54.00%	2.80%	8.66%	0.00%	NA
All Indica	492	54.70%	0.20%	8.74%	0.00%	NA
All Japonica	244	50.80%	7.60%	8.61%	0.00%	NA
Aus	7	71.40%	0.00%	14.29%	0.00%	NA; AA: 16.70%
Indica I	492	54.70%	0.20%	8.74%	0.00%	NA
Indica II	215	68.80%	0.50%	6.51%	0.00%	NA
Indica III	21	66.70%	0.00%	9.52%	0.00%	NA; AA: 26.30%
Indica Intermediate	190	49.50%	0.00%	10.53%	0.00%	NA; AA: 44.70%
Temperate Japonica	189	53.40%	0.60%	8.47%	0.00%	NA
Tropical Japonica	36	0.00%	41.70%	8.33%	0.00%	NA; AA: 18.20%
Japonica Intermediate	19	57.90%	5.90%	10.53%	0.00%	NA
VI/Aromatic	9	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	231	50.20%	1.40%	10.39%	0.00%	NA

Showing 1 to 13 of 13 entries

Contact

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

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Search for Variation information by Variation ID:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

RiceVarMap v2.0

Tools

Blast

Design Primer by Variation ID

Design Primer by Region

Haplotype Network Analysis

Varitation Coordinate Convert

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