Quality Value Limit

The Quality Value Limit is the threshold setting to which bases will be scored accurately. If a QV setting of 10 is selected, the base caller will assign a base call to each peak it recognises and gives a confidence score with each base, blue being very confident, yellow is relatively confident and red is less confident. If the base caller cannot identify a valid base an N will be assigned. If a QV setting of 20 or 30 is selected, the base calling becomes more stringent, removing the yellow and red confidence bars and only offering blue confident base calls or N base calls.

Mixed Base Identification

Mixed bases are one-base positions that contain two or more bases. If the mixed base identification is selected the base caller assigns an IUB code to every base that contains a second peak at the same position which is >25% of the largest peak. If the mixed base identification is not selected, the base caller assigns an A, C, G or T to every peak. Bases that have a quality value < than the QV setting selected (10, 20 or 30) will be assigned an N.

IUB codes

A – Adenine

C – Cytosine

G - Guanine

T - Thymine

B – C or G or T

D – A or G or T

H – A or C or T

V – A or C or G

R – A or G

Y – C or T

K – G or T

M – A or C

S – G or C

W – A or T

N – any base

Quality Clipping

The start and end of a sequence read can be difficult for the base caller to accurately assign bases to the peaks. The Quality Clipping setting is the removal of the start and end base calls until fewer than a set number of bases have a QV setting of less than the default.


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