More docs on the ARB website. See also index of helppages. Last update on 04. Mar 2022 .
Main topics:
Related topics:

# Calculate the Percentage of the Most Frequent Base

## DESCRIPTION

### Finds the most frequent base (or gap) in each column for all marked species. Then the number of all sequences with this base are divided by:

• the number of all marked sequences (if not ignoring gaps)
• the number of bases in this column (if ignoring gaps)

### The resulting percentage is divided by ten and then the second last digit is taken:

```0%  - 19%  ->  '1' (does not occur for nucleotides)
20% - 29%  ->  '2'
30% - 39%  ->  '3'
...
90% - 99%  ->  '9'
100%       ->  '0'```

## NOTES

### Internally the SAI consists of two lines: the main line called 'data' and a second line called 'dat2'.

The first is used when you use the SAI as conservation profile or filter and contains the SECOND LAST digit of the calculated frequencies.
The second contains the LAST digit of the calculated frequencies. It is not used and does only show up, when you load the SAI into ARB_EDIT4, where it will show both lines.

## EXAMPLES

### Say one column contains 7 A's 4 G's and 5 Gaps.

• ignoring gaps will result in 7/11 == 64 % which is converted to '6'.
• otherwise we get 7/16 == 44% which will be indicated by a '4' in the target sequence.

## Ambiguities

### Ambiguities are counted proportionally, i.e.

• a 'N' counts as 1/4 'A', 1/4 'C', 1/4 'G' and 1/4 'T'
• a 'D' counts as 1/3 'A', 1/3 'G' and 1/3 'T'
• a 'Y' counts as 1/2 'C' and 1/2 'T'

### Example:

A column containing 9 'C' and one 'Y' results in a max. frequency of 95% (=9.5 'C').