Human vs Ma's night monkey LastZ results
Human (Homo sapiens, GRCh38) and Ma's night monkey (Aotus nancymaae, Anan_2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 91. 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) | 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) | Primate:
A C G T
90 -330 -236 -356
-330 100 -318 -236
-236 -318 100 -330
-356 -236 -330 90
|
Chunking parameters
| Parameter | Human | Ma's night monkey |
|---|---|---|
| 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 1,279,243 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 911,508,114 out of 3,099,750,718 |
Uncovered: 1,230,374 out of 38,571,754 |
| Ma's night monkey |
Uncovered: 768,289,723 out of 2,861,668,348 |
Uncovered: 1,777,072 out of 33,534,099 |
Block size distribution
| Size range | All 1,279,243 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 31,768 |
177.7 kb |
|||
| 10 bp - 100 bp | 89,967 |
4.8 Mb |
20,516 |
1.2 Mb |
|
| 100 bp - 1 kb | 514,358 |
244.4 Mb |
45,889 |
15.2 Mb |
|
| 1 kb - 10 kb | 629,150 |
1.8 Gb |
16,393 |
42.8 Mb |
|
| 10 kb - 100 kb | 14,000 |
182.8 Mb |
2,047 |
54.8 Mb |
|
| 100 kb - 1 Mb | 391 |
147.7 Mb |
|||
| 1 Mb - 10 Mb | 379 |
1.4 Gb |
|||
| 10 Mb - 100 Mb | 43 |
624.2 Mb |
|||