Human (Homo sapiens, GRCh37) and Chimpanzee (Pan troglodytes, CHIMP2.1) were aligned using the BlastZ alignment algorithm (Schwartz S et al., Genome Res.;13(1):103-7, Kent WJ et al., Proc Natl Acad Sci U S A., 2003;100(20):11484-9) in Ensembl release 55. Human was used as the reference species. After running BlastZ , the raw BlastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.
Full list of pairwise alignments| Gap open penalty (O) | 600 | ||||||||||||||||||||
| Gap extend penalty (E) | 150 | ||||||||||||||||||||
| HSP threshold (K) | 4500 | ||||||||||||||||||||
| Threshold for gapped extension (L) | 2200 | ||||||||||||||||||||
| Threshold for alignments between gapped alignment blocks (H) | 2000 | ||||||||||||||||||||
| Masking count (M) | 50 | ||||||||||||||||||||
| Seed and Transition value (T) | 2 | ||||||||||||||||||||
| Scoring matrix (Q) |
|
Number of alignment blocks: 692174
| Genome coverage(bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
|
|
| 2,263,640,977 out of 3,098,825,702 | 34,385,806 out of 35,483,623 | |
| Chimpanzee |
|
|
| 2,220,936,942 out of 3,350,413,343 | 31,889,779 out of 32,180,345 |