RiceVarMap2

Search for Variation information by Variation ID:

Flanking Sequence (100 bp) in Reference Genome:

TTGTGAGCACTCAGAACAGGAAGTTCTCCATTCATGGTCAAGGCAACAACAAATGCTCCTGCCAGCTGGCAGTCAGCAATGAAATGATTTAAGGGAACTC[CAAACAA/CAAACAG]
ACATAACCCTATCCACTTAAGCATAACAATTCTAACGTTCAAAGAATCACTAACAAATGCGGAACTTATTTATTCATAGCTTCAGAACTATTTGATGACG

Reverse complement sequence

CGTCATCAAATAGTTCTGAAGCTATGAATAAATAAGTTCCGCATTTGTTAGTGATTCTTTGAACGTTAGAATTGTTATGCTTAAGTGGATAGGGTTATGT[TTGTTTG/CTGTTTG]
GAGTTCCCTTAAATCATTTCATTGCTGACTGCCAGCTGGCAGGAGCATTTGTTGTTGCCTTGACCATGAATGGAGAACTTCCTGTTCTGAGTGCTCACAA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of CAAACAA(primary allele)	Frequency of CAAACAG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	774	90.70%	6.80%	2.71%	0.00%	NA
All Indica	492	97.80%	0.40%	1.83%	0.00%	NA
All Japonica	244	76.60%	20.10%	4.10%	0.00%	NA
Aus	7	85.70%	0.00%	14.29%	0.00%	NA
Indica I	492	97.80%	0.40%	1.83%	0.00%	NA
Indica II	215	99.10%	0.50%	0.47%	0.00%	NA
Indica III	21	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	190	96.80%	0.50%	2.63%	0.00%	NA
Temperate Japonica	189	72.50%	23.90%	4.76%	0.00%	NA
Tropical Japonica	36	91.70%	5.70%	2.78%	0.00%	NA
Japonica Intermediate	19	89.50%	10.50%	0.00%	0.00%	NA
VI/Aromatic	9	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	231	95.20%	2.20%	2.60%	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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