1. Select the organism & genome version

CandiSNP will classify your SNPs from the genome annotations you choose

2. Click to select or drop a data file to begin

Download some sample data to examine and use

Control Panel

    Choose spot colours
  • Non-synonymous coding CT/GA
  • Non-synonymous coding
  • Annotated region
  • Non-annotated region
  • CDS
  • Set allele frequency range

    Download SVG
    Download PNG
    Download Annotated SNPs


    1. Pre-processing your SNP data

    CandiSNP works on pre-processed, filtered, high-confidence SNPs that you provide, there are lots of ways of preparing SNP data. Here are some hints on how to go about this:

    2. Selecting a genome

    The genome annotations for TAIR10, TAIR9, Rice genome v7, Tomato genome v2.40, Glycine max genome 1.09v8, Grape genome v1 and Maize B73 v5b are currently available in CandiSNP. It is essential that the chromosome names in column 'Chr' match that in the database. Here are the chromosome names for each genome build:

    GenomeChromosome names
    TAIR101, 2, 3, 4, 5, M, C
    TAIR91, 2, 3, 4, 5, M, C
    Rice genome v71, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, Un, Sy
    Tomato genome v2.40SL2.40ch00, SL2.40ch01, SL2.40ch02, SL2.40ch03, SL2.40ch04, SL2.40ch05, SL2.40ch06, SL2.40ch07, SL2.40ch08, SL2.40ch09, SL2.40ch10, SL2.40ch11, SL2.40ch12
    Glycine max genome 1.09v8Gm01, Gm02, Gm03, Gm04, Gm05, Gm06, Gm07, Gm08, Gm09, Gm10, Gm11, Gm12, Gm13, Gm14, Gm15, Gm16, Gm17, Gm18, Gm19, Gm20 and 21 to 2287
    Grape genome v11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1_random, 10_random, 11_random, 12_random, 13_random, 16_random, 17_random, 18_random, 3_random, 4_random, 5_random, 7_random, 9_random
    Maize B73 v5b1, 4, 2, 3, 5, 7, 8, 6, 9, 10, UNKNOWN, Mt, Pt

    3. Upload

    Once your file is prepared click or drop your file into the 'Click to select or drop a data file to begin' area. Upload will begin and your data will be analysed. When it is done, an interactive plot will be displayed on the screen.

    4. Control Panel

    When the plot appears, a control panel to determine it's data and appearance is also displayed, it has four sections

    5. The Plot

    You will see a plot like this for every contig or chromosome of your chosen assembly.

    6. Plotting Tips