One such reads thus: "Do You Know That Polar Bears Are Found Only At the North Pole Penguins Only at the South Pole.
We mapped such reads onto the O. sativa Japonica Nipponbare chloroplast sequence, called SNPs and indels and constructed a neighbor-joining tree.
Annotation of such reads revealed that almost 50% of them were related to antibiotic and toxic compounds resistance genes, which are extremely important features for microbial survival and adaptation in polluted environments.
Such reads are considered "mapped".
We prefer to remove such reads altogether.
Such reads are not long enough to depict miRNA precursors, which are usually longer than 50nt.
We started with over 1.5 billion such reads from the H1 embryonic stem cell line generated on the Illumina GAII sequencer [21].
There are two sources of such reads: 1) reads with a second piece fewer than eight bases long and 2) reads where the second piece matched equally well to multiple locations within the maximum intron size.
The crude analysis have shown that the average coverage is similar in all chromosomes (mean = 0.03 and standard deviation = 0.007) suggesting that such reads do not originate from a specific locus in a genome.
We selected a sequence coverage of 0.1x and 25 bp read lengths with a 1% error rate because technology will be available soon to produce such reads from an entire mammalian genome in a single run.
Such reads may represent highly conserved sequences that hit multiple genomes making unambiguous mapping impossible, had too few high-quality bases, or they may represent an unknown source of sequence library contamination.
