RiceVarMap2

Search for Variation information by Variation ID:

Flanking Sequence (100 bp) in Reference Genome:

CTCCATCTGACAAACTAATACAGCAATACTACTATACAATACAATCAGTAACGAGATCTCTGCCTGCACAGAACGAAATCGGTTGCAAATCACCCAGGGG[AA/AAA,AAAA]
AAAATACTACTGAAAAAAGAAGAGCAACAATCTCCAGTTTCTTTCTGGGCAAAATGTGCATCATTCTTGTCTGATCAGACGTGAGGAGCTGAGCTCTGTG

Reverse complement sequence

CACAGAGCTCAGCTCCTCACGTCTGATCAGACAAGAATGATGCACATTTTGCCCAGAAAGAAACTGGAGATTGTTGCTCTTCTTTTTTCAGTAGTATTTT[TT/TTT,TTTT]
CCCCTGGGTGATTTGCAACCGATTTCGTTCTGTGCAGGCAGAGATCTCGTTACTGATTGTATTGTATAGTAGTATTGCTGTATTAGTTTGTCAGATGGAG

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	50.40%	0.30%	8.91%	0.00%	NA
All Indica	492	75.40%	0.20%	5.69%	0.00%	NA
All Japonica	244	2.40%	0.00%	15.16%	0.00%	NA; AAA: 82.80%
Aus	7	85.70%	14.30%	0.00%	0.00%	NA
Indica I	492	75.40%	0.20%	5.69%	0.00%	NA
Indica II	215	62.80%	0.00%	7.44%	0.00%	NA; AA: 32.20%
Indica III	21	95.20%	0.00%	4.76%	0.00%	NA
Indica Intermediate	190	78.90%	0.60%	5.79%	0.00%	NA
Temperate Japonica	189	0.00%	0.00%	16.40%	0.00%	NA; AA: 0.00%; AA: 83.60%
Tropical Japonica	36	12.10%	0.00%	8.33%	0.00%	NA; AAA: 80.60%
Japonica Intermediate	19	6.20%	0.00%	15.79%	0.00%	NA; AAA: 78.90%
VI/Aromatic	9	0.00%	0.00%	11.11%	0.00%	NA; AA: 0.00%; AA: 88.90%
Intermediate	231	68.80%	0.50%	7.36%	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

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

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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