This assembly highlighted several features of PRICE, primarily its ability to accommodate hugely inconsistent read coverage levels, even across a single transcript.
A BAC was not considered complete until all inconsistent read pairs were resolved and Consed reported an error rate of less than 1/10,000 bases.
Regions with significantly higher or lower coverage (log 2 > 0.75 or log 2 < –0.75) and/or having inconsistent read pairing were manually inspected to discard possible assembly or mapping artifacts (see Materials and Methods).
Genes in which the fpkm standard deviation (SD)/mean >1 within the replicates were excluded, since analyses of reads suggested that the divergence in such cases was usually due to inconsistent read alignment in the presence of nearby or overlapping genes.
REAPR and ALE analysis also show some remaining problematic areas in the CB4856 reference, including high read coverage in regions that suggests unresolved duplications (sometimes overlapping more than one JR contig with poor alignment scores), low coverage, and inconsistent read pairing.
Without even being aware of Hennig's work, David Hull (1964) pointed out that this approach resulted in classifications that were logically inconsistent (read illogical) with the phylogenies they were supposed to summarize.
Students are asked to analyze data that appears inconsistent, to read for irony, to explore the unknown.
One explanation for why putamen activation is inconsistent across reading studies is that its involvement depends on the reading strategy used.
Given the poor, and potentially inconsistent representation of reads associated small non-coding RNA genes in our study, these genes are excluded from further analysis.
Comparisons of Illumina and Sanger sequencing revealed two inconsistencies: site 23 in PmaNZ058, and site 12,982 in PmaNZ005 (no longer inconsistent when duplicate Illumina reads were removed), giving a total Illumina-Sanger discrepancy rate of two inconsistencies in 57,240 bp compared or 0.0034%.
