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Alternatively, the ChemSpider Combined Reference Scoring term ((S_{C_{{mathrm{CCR}}}})) can be calculated, as shown below in Eqs.
In each case, analyses were made comparing 577XX (reference group) vs. 577RX, 577XX vs. 577RR (co-dominant effect), 577XX vs. 577RR and 577RX combined (dominant effect), and 577XX and 577RX combined (reference group) vs. 577RR (recessive effect).
Surprisingly, the variant calling FNR of the combined reference strategy was higher with BWA alignment.
Both programs equally identified TBP and HPRT1 as the most stable combined reference genes.
The expression of each candidate gene for each sample was normalized to the combined reference genes.
The direct mapping strategy also missed a lot more true non-synonymous SNVs than the combined reference strategy.
Such a combined reference standard has been considered appropriate for cervical cancer test accuracy studies given ethical and other issues involved in performing biopsy for test-negatives [ 13].
To this end, the idea of a combined reference standard, as the one proposed above, can improve our capacity to identify and manage growth-restricted babies appropriately.
While the filtering strategy did not identify any false non-synonymous SNVs and the combined reference strategy identified 3, the direct mapping strategy identified 47 of them.
A combined reference standard was developed incorporating biopsy results when available; negative colposcopy was accepted as a negative outcome when no biopsy was taken.
Figure 1 shows the imputation accuracy across BTA29 for the two most accurate scenarios, i.e. BEAGLE and IMPUTE2 with genotype probability data and a combined reference population.
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