Analysis Output | Base Call Codes

Base Call Codes

The mtDNA Processor App supports variant calling for more than one nucleotide at a position. When more than one nucleotide exceeds the interpretation threshold, the app reports the IUPAC code as the consensus for the position.

Table 2    Variant Base Call Codes1 Table

Code

Base

A

Adenine

C

Cytosine

G

Guanine

T

Thymine

R

A or G

Y

C or T

S

G or C

W

A or T

K

G or T

M

A or C

B

C or G or T

D

A or G or T

H

A or C or T

V

A or C or G

N

Any base

-

Deletion

*

No call

When data for the indel and a base call at a position exceed the interpretation threshold, the app reports the ambiguous call code for an indel as the consensus for the position.

Table 3    Ambiguous Variant Base Call Codes Table

Code

Base

a

Adenine

c

Cytosine

g

Guanine

g

Thymine

r

a or g

y

c or t

s

g or c

w

a or t

k

g or t

m

a or c

b

c or g or t

d

a or g or t

h

a or c or t

v

a or c or g

n

Any base

1Codes are from the International Union of Pure and Applied Chemistry (IUPAC).

For example, Figure shows the presence of an ambiguous deletion at position 501. Because there are an equal number of reads that support a deletion call and a reference call of G, the app reports an ambiguous call of g as the consensus.

Figure Example of Ambiguous Variant Base Calls