RiceVarMap2

Search for Variation information by Variation ID:

Flanking Sequence (100 bp) in Reference Genome:

GCTAAGTTCCCTATTTGATAGGCCAAGTTCCTAAATTAAAATAGCTGCATATATTCGGTTGGATATAGAGACCGGGTAAAAAATACCCTTCTCTAAAAAA[ATATATATTTCC/ATATATGTTTCC,ATATATATTTCT]
ATTCATCTATCCTCTCTTGAAATATTGTGGCAGGGTAAAAAATACCCTTCTCTAAAAAAATATATATTTCCATTCATCTATCCTCTCTTGAAATATTGTG

Reverse complement sequence

CACAATATTTCAAGAGAGGATAGATGAATGGAAATATATATTTTTTTAGAGAAGGGTATTTTTTACCCTGCCACAATATTTCAAGAGAGGATAGATGAAT[GGAAATATATAT/GGAAACATATAT,AGAAATATATAT]
TTTTTTAGAGAAGGGTATTTTTTACCCGGTCTCTATATCCAACCGAATATATGCAGCTATTTTAATTTAGGAACTTGGCCTATCAAATAGGGAACTTAGC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of ATATATGTTTCC(primary allele)	Frequency of ATATATATTTCC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	774	54.80%	36.50%	13.70%	0.00%	NA
All Indica	492	82.50%	6.50%	11.79%	0.00%	NA
All Japonica	244	4.80%	82.00%	13.93%	0.00%	NA
Aus	7	16.70%	71.40%	14.29%	0.00%	NA
Indica I	492	82.50%	6.50%	11.79%	0.00%	NA
Indica II	215	88.80%	0.50%	10.70%	0.00%	NA
Indica III	21	81.00%	0.00%	19.05%	0.00%	NA
Indica Intermediate	190	76.80%	9.30%	15.26%	0.00%	NA
Temperate Japonica	189	4.30%	83.10%	13.23%	0.00%	NA
Tropical Japonica	36	7.10%	72.20%	22.22%	0.00%	NA
Japonica Intermediate	19	5.60%	89.50%	5.26%	0.00%	NA
VI/Aromatic	9	0.00%	0.00%	88.89%	0.00%	NA; ATATATGTTTCC: 88.90%
Intermediate	231	66.20%	21.90%	15.15%	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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