Human self-LastZ results
Human (Homo sapiens, GRCh38) was aligned to itself using the LastZ alignment algorithm (LastZ) in Ensembl release 76. After running LastZ, alignments between the same locations were removed and the remaining raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Self-alignments reveal duplicated regions: some being recent and almost identical, others being much older and indicators of ancient whole-genome duplications.
Configuration parameters
| Parameter | Value |
|---|---|
| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 5000 |
| Threshold for gapped extension (L) | 5000 |
| Threshold for alignments between gapped alignment blocks (H) | 3000 |
| Masking count (M) | 10 |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | $ENSEMBL_ROOT_DIR/ensembl-compara/scripts/pipeline/primate.matrix |
Chunking parameters
| Parameter | Human (reference) | Human (non-reference) |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options |
Statistics over 186,172 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 2,777,232,633 out of 3,099,750,718 |
Uncovered: 31,042,982 out of 38,571,754 |