Deduction for sub standard work at the time of SES

Sir,

Is there any means by which we can add deductions against some sub standard work at the time of SES.

For eg.  If OFC cable was to be laid for 10 Km @50 at requisite depth.

suppose contractor does the work for whole 10 Km but at lesser depth. we want to impose penalty of Lumpsum amount(say 30).

Now at the time of SES if i verify full quantity full amount is verified. i.e 500 (10*50),but iwant to verify 500-30 =470 only.

In previous threads it was suggested to verify quantity amounting to 470 i.e 10-30/500*10=9.4 which is ideally incorrect.

My System Integrator says in standard SES (ML81N) deductions is standard field but it does not affect calculation..

Kindly guide how this deduction amount be deducted from total amount.