RiceVarMap2

Search for Variation information by Variation ID:

Flanking Sequence (100 bp) in Reference Genome:

CTACCGGATGAAAGTGGAAATCCAACTGAAAGGGCTAAGGTGAAAATAGGACACATGCATGCATGACGAGGTAGGTTAATTATGTACAGAATCTATATTA[CAAGC/CAAGG]
AAGCAATGAATGATCACCTTCGTTGTAATCTTTGATCAGCAGGTCTTGCAGTTCCAGTGGTCTCAGCTTCTCCCTCCATGTCATCATCATCTGACTGCTC

Reverse complement sequence

GAGCAGTCAGATGATGATGACATGGAGGGAGAAGCTGAGACCACTGGAACTGCAAGACCTGCTGATCAAAGATTACAACGAAGGTGATCATTCATTGCTT[GCTTG/CCTTG]
TAATATAGATTCTGTACATAATTAACCTACCTCGTCATGCATGCATGTGTCCTATTTTCACCTTAGCCCTTTCAGTTGGATTTCCACTTTCATCCGGTAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of CAAGG(primary allele)	Frequency of CAAGC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	774	57.80%	37.70%	7.36%	0.00%	NA
All Indica	492	88.40%	4.80%	7.11%	0.00%	NA
All Japonica	244	1.30%	92.20%	6.56%	0.00%	NA
Aus	7	0.00%	85.70%	14.29%	0.00%	NA
Indica I	492	88.40%	4.80%	7.11%	0.00%	NA
Indica II	215	90.70%	3.00%	6.51%	0.00%	NA
Indica III	21	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	190	82.60%	8.20%	10.00%	0.00%	NA
Temperate Japonica	189	1.10%	92.10%	6.88%	0.00%	NA
Tropical Japonica	36	2.90%	91.70%	5.56%	0.00%	NA
Japonica Intermediate	19	0.00%	94.70%	5.26%	0.00%	NA
VI/Aromatic	9	0.00%	88.90%	11.11%	0.00%	NA
Intermediate	231	71.90%	19.80%	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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