Human vs Alpine marmot LastZ results
Human (Homo sapiens, GRCh38) and Alpine marmot (Marmota marmota marmota, marMar2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 96. Human was used as the reference species. After running LastZ, the 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.
Configuration parameters
| Parameter | Value |
|---|---|
| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 3000 |
| Threshold for gapped extension (L) | 3000 |
| Threshold for alignments between gapped alignment blocks (H) | 2200 |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | Default:
A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91
|
Chunking parameters
| Parameter | Human | Alpine marmot |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 2,179,285 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 1,517,263,017 out of 3,099,750,718 |
Uncovered: 2,051,842 out of 38,571,754 |
| Alpine marmot |
Uncovered: 1,048,563,005 out of 2,510,587,379 |
Uncovered: 1,875,208 out of 31,034,716 |
Block size distribution
| Size range | All 2,179,285 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 70,857 |
474.6 kb |
|||
| 10 bp - 100 bp | 265,189 |
12.6 Mb |
17,173 |
1.2 Mb |
|
| 100 bp - 1 kb | 1,297,529 |
580.5 Mb |
62,060 |
21.9 Mb |
|
| 1 kb - 10 kb | 545,024 |
1.1 Gb |
22,191 |
54.6 Mb |
|
| 10 kb - 100 kb | 681 |
9.6 Mb |
1,596 |
37.5 Mb |
|
| 100 kb - 1 Mb | 5 |
579.3 kb |
165 |
59.9 Mb |
|
| 1 Mb - 10 Mb | 135 |
541.3 Mb |
|||
| 10 Mb - 100 Mb | 47 |
941.1 Mb |
|||