We could only attach to each human gene a p-value for the excess of mismatches with gene inactivating potential in cancer samples.
Individuals were excluded for excess autosomal heterozygosity, mismatches between called and phenotypic gender, and if there were outliers identified by an IBS clustering analysis.
The sum is a bit in excess because two mismatches in the second repeat disqualify the repeat block as a triple tandem repeat.
Thirdly, we provide an exploratory analysis of the causes of excess kindergarten travel and spatial mismatch.
Samples with a low call rate, with excess autosomal heterozygosity, with sex-mismatch, or outliers identified by the identity-by-state clustering analysis were excluded.
The observed misincorporation pattern was in agreement with that expected for ancient DNA molecules, ie. an excess of G to A mismatches at the 5'-ends of reads.
Interestingly, the new population of hits identified for both platforms shows an excess of cytosine deamination related mismatches at 5'-ends (C → T for Illumina and G → A for Helicos, Additional file 1: Figure S1, S2), suggesting that these most likely consist of DNA templates with 5'-overhangs, that were lost due to the use of a seed region.
Furthermore, any dimer species that is seen in radiolabeled gel analysis can be attributed to the presence of extreme excess unlabeled strands allowing for a mismatch in concentrations between each individual strand and were therefore ignored.
Overall, the observed excess was greatest with zero allowed mismatches and least with two.
Negative controls were prepared by omitting the primary antibodies, pre-adsorbing the primary antibodies with an excess of antigen when available, and mismatching the secondary antibodies.
