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Of the 48 variant positions with an inconsistent call in the 4 replicates we closely examined the reason for this discordance from the raw sequencing data.
However, 77 positions had an inconsistent call between the two data sets; particularly 76 were called as indels in our data but were called as a SNP in the 1000 bulls data (Table 6).
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We observed a very low rate at which homozygous SNPs over-called as heterozygous (0.1 0.2 %), heterozygous SNPs under-called as homozygous (0.2 0.4 %) and of inconsistent calls (≤4 per cow) (Tables 3 and 4).
"The result is inconsistent call-taking operations that can have an impact on response times and may also lead to incorrect resources being sent to an incident," the report said.
"He's made inconsistent calls, and frustration has mounted," said the staff assistant, who would not agree to be named.
In addition, all SNPs were set to "missing" in case of Mendelian inconsistent calls within a family.
In a set of biological replicates, MAS5 produced inconsistent calls for twice as many probe sets as the GM algorithm.
In contrast, the GM algorithm consistently assigned the same Up/Down call for each of 19,923 probes and gave inconsistent calls for the remaining 2359 probes.
Pilot participants with inconsistent calls across methods were assigned 'no call' at the SNP, which resulted in 2 missing genotypes at mt204 and 1 at mt228.
Of the 22,283 probes examined in the experiment, the MAS5 algorithm was consistent in assigning the same Present/Absent call, across all samples, for each of 17,004 probes; the remaining 5278 probes were assigned inconsistent calls by MAS5.
Only 40 60% of the M>B probes were consistently assigned to the same genotype across independent replicates and the rate of inconsistent calls between the replicates was higher (Table 1).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com