> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/annotation/v3.27/data-sources/cpg-island.md).

# CpG Island

### Overview

This supplementary data is one of the supplementary data that will only be used for annotating methylation gVCF file. In general, this supplementary data define genoimic region interval that indicates CpG island. The suppplementary data is available for both GRCh37 and GRCh38. Both data is obtained from publicly available source from UCSC FTP.

[File URL for GRCh37](https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/cpgIslandExt.txt.gz)

[File URL for GRCh38](https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cpgIslandExt.txt.gz)

The file schema is explained in this [link](https://genome.ucsc.edu/cgi-bin/hgTables?db=hg38\&hgta_group=regulation\&hgta_track=cpgIslandExt\&hgta_table=cpgIslandExt\&hgta_doSchema=describe+table+schema\&token=0.3AJvdi8lQklpZoYaOvLfRQTg59D9FBChXYDeKnuzwNYx_K4ngeQAYTvkozqVpet2lf8_JlEhxW6UdvmGc2kwtI6dT-4GozhaTk-cMSSa-z-c8XOe1xme8Af23gho5FyU350UFwgfX2MiXQ988-H7o6ihL5cnIrDTcQlhueTSr_PF1CLwG8JcQhe-ChIAj830FlSLYnO2NZAxV3AFMaHMh5e56lmr1jdguhgeHfdixl4Xd5xfjCy08rrwimKpcxpUMrJa1vI6M00J-Db9hF86JIh7aiKGKk26Uoiy1gm6J2AAwogP49dg99g-GcQZoFhP6WvZAO1PHnjbNUkUSaw01QXYo6Qdq6V28QtaFlBXi4Z_yruOGL8EUU3iFbrzCMUm3LevEsy7FxfwoyJ2VWGLXjlhr4EGpMR4-J7yHZ8V40xUlOyNzC3JjLkzR5lEg8OkQLJirGHXKAoO7jUh8qXNS2HCmB-SS1GzDJBFQrNcolXQPaQVr_5Rver0Qwv4-VIK2GmFS89lzP65xJONna7_XInb1OTz_p-jGIjV_1DRbNhCa1wNLXXQ3I7G589BlTqjftzDUgaZUpTV-EYHP_Z2IH5lYS94ns13Rxz7Nclr048LdkSpkfsVy1G7LmGIgYMT7-FC39cu6sbIGI2KQH7H90xbMcjtOJ6zRS4awug-4_RRGfM8EiQvSfsWGPKAcUNXtBMvHc0WfqwhpnOay0UHtfOADtev0pnVg07bHl0h5GmbWVuU8WkDC5dLBPtZEUgWNAYSceOb0x8Qgqmxx2X2-UlBT-CZlLCd1MM9WmD5riuDCQSz1F15GqkA-ZezxqVL5TdUti3EzgZWuDTB4qSrVGau_fkz8iwumjXUJsKSq52Y9jc0GKjKWGgpq8cc18WbjRsSK8T3N-ma9FMQsZN0OaS4gSBHoLCSfhTnldhHWcUEXFBU8oYaSKtRZP76Ngg-.DHbWsXcNG2gbaQJ6c45otA.8ab9bf6345609f9a3a4fdfbb33bf775632b38277175e4924bebb2c9d3c278448)

### Parsing

From those TSV file, we read every entry and store all info so that we can produce those data in the output.

### Output

An example of methylation annotation from CpG Island region is below

```
{
  "chromosome": "21",
  "begin": 20997105,
  "end": 20998245,
  "regionId": "CpG: 89",
  "biotype": "cpgIsland",
  "bin": 745,
  "length": 1140,
  "cpgNum": 89,
  "gcNum": 674,
  "percentageCpg": 15.6,
  "percentageGc": 59.1,
  "observedToExpectedRatio": 0.89,
  "samples": [
    {
      "sampleId": "mate_len_200bp_100X",
      "averageCpGMethylation": 0.5085069662921352,
      "totalCpGCoverage": 5413,
      "totalCpGPosition": 44.5
    }
  ]
}
```

The output includes the biotype `cpgIsland` and contains additional fields derived from the supplementary data.

The following table describes these extra fields:

| Field                     | Description                                                       |
| ------------------------- | ----------------------------------------------------------------- |
| `bin`                     | Indexing bin used for efficient spatial querying.                 |
| `length`                  | Total length of the CpG island region.                            |
| `cpgNum`                  | Number of CpG dinucleotides within the island.                    |
| `gcNum`                   | Number of G and C nucleotides within the island.                  |
| `percentageCpG`           | Percentage of CpG dinucleotides in the region.                    |
| `percentageGc`            | Percentage of GC content in the region.                           |
| `observedToExpectedRatio` | The ratio of observed to expected CpG counts.                     |
| `regionId`                | Corresponds to the `name` column from the original UCSC TSV file. |


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