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The CCDS database, therefore, has some tolerance for minor differences between the NCBI and EBI/WTSI annotations (though not affecting the start, stop or splice site locations), with these differences being due to sequence polymorphisms between the reference genome sequence and the transcript data or publication support the RefSeq is based on.
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This was done to determine if the failure to detect MITEs is due to sequence divergence or if they are preferentially amplified in O. brachyantha.
We did not determine however, whether this was due to sequence mosaicism or horizontal gene transfer.
Most likely, this deviation is due to sequence bias in the library.
The discrepancy in responses to HL9 might be due to sequence heterogeneity in different viral clades.
Most likely this variability is due to sequence specificity of RNAse cleavage and/or adapter ligation.
This indicates that the loss of the KRAB domain in dog was due to sequence degeneration.
The remaining false negatives are due to sequence divergence, microarray technical error, or a variable that we did not quantify.
However, we cannot exclude that some low-abundance subject-specific 100%-ID phylotypes identified were due to sequence errors.
The loss of colinearity is due to sequence divergence and the movement of transposable elements since the duplication event.
Most variation in gdh and ITS were due to sequence diversity within individuals, followed by sequence variations among individuals with virtually little sequence variation due to geographic origin.
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