Marker from large set with certain prefix in CottonGen have been standardized by number of digits (based on the size of marker dataset). This table lists the rules of standardization.
Note: To distinguish with the markers using 4-digit in the standardization, marker with 3- or 5-digit displayed in red or blue in the table.
| Type | Marker set prefix | Num. of digits | Example |
| SSR | BNL | 4 | BNL0001 |
| SSR | C2- | 5 | C2-00001 |
| SSR | CCRI | 4 | |
| SSR (EST-SSR) | CER | 4 | CER0001 |
| SSR | CGR | 4 | ... |
| SSR | CIR | 4 | ... |
| SSR | CM | 4 | ... |
| SSR | CMS | 4 | ... |
| SSR | COT | 3 | COT001 |
| SSR | CHSE | 4 | ... |
| SSR | DC | 5 | ... |
| SSR | DOW | 3 | ... |
| SSR | DPL | 4 | ... |
| SSR | Gh | 3 | ... |
| SSR (EST-SSR) | HAU | 4 | ... |
| SSR | JESPR | 4 | ... |
| SSR (EST-SSR) | MGHES | 4 | ... |
| SSR (EST-SSR) | MUCS | 4 | ... |
| SSR | MUSB | 4 | ... |
| SSR (EST-SSR) | MUSS | 4 | ... |
| SSR (EST-SSR) | NAU | 4 | ... |
| SSR | NBRI_ | 4 | NBRI_0001 |
| SSR (EST-SSR) | NBRI_e | 4 | NBRI_e0001 |
| SSR (EST-SSR) | SHIN- | 4 | SHIN-0001 |
| SSR (EST-SSR) | STV | 4 | ... |
| SSR | SWU | 5 | ... |
| SSR | TMB | 4 | ... |
| SSR | UCD | 3 | ... |
| SRAP | CF | 4 |