At these locations, we estimated the overlap for individual SNP calls, i.e., chr/pos/ref/alt and for no calls; i.e., chr/pos/ref/ref; between sequencing and array platforms (Additional file 16).
We amplified and sequenced the cytochrome b fragment (as described in [ 29]) in 34 of the 36 individuals used in the aCGH, counted the number of actual mismatches between the obtained sequences and array probes, and compared the hybridization signal intensities between probes with different numbers of mismatches.
Therefore, the possibility that the correlation between mate pair sequencing and array painting is caused by intrinsic characteristics of chromosomes could be ruled out.
To better understand the disagreement between the cDNA sequencing and array results, we performed qPCR on a large subset of genes.
For instance, there seems to be general confusion amongst clinicians around the distinction between genomic sequencing and array-based genotyping.
This poses certain challenges for sequencing and array platforms.
In addition, the average nucleotide identity between the wVitB genes captured and wPip is 95.7% and the lowest nucleotide similarity between the wVitB sequence and the array sequence is 78.5% (316 bp of a transposase sequence), indicating the array methodology is sufficient to pull-down sequences of closely related strains, species, or even genera.
For comparison, the discordant rate between HapMap sequencing genotypes and array genotypes is 4% in the 7816 SNP/sample combinations that had a non-N call in both data sets.
As a cross validation between sequencing and genotyping data, 22 SNP markers of the SolCAP array overlapped the re-sequenced regions.
In addition, the average nucleotide identity between the w VitB genes captured and w Pip is 95.7% and the lowest nucleotide similarity between the w VitB sequence and the array sequence is 78.5% (316 bp of a transposase sequence), indicating the array methodology is sufficient to pull-down sequences of closely related strains, species, or even genera.
