Human vs Golden snub-nosed monkey LastZ results
Human (Homo sapiens, GRCh38) and Golden snub-nosed monkey (Rhinopithecus roxellana, Rrox_v1) 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 | Golden snub-nosed monkey |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 848,421 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 552,589,180 out of 3,096,649,726 |
Uncovered: 379,434 out of 35,444,608 |
| Golden snub-nosed monkey |
Uncovered: 458,090,885 out of 2,899,552,139 |
Uncovered: 1,053,026 out of 33,867,875 |
Block size distribution
| Size range | All 848,421 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 17,986 |
99.6 kb |
|||
| 10 bp - 100 bp | 59,174 |
3.0 Mb |
15,788 |
928.1 kb |
|
| 100 bp - 1 kb | 241,928 |
112.0 Mb |
42,421 |
14.2 Mb |
|
| 1 kb - 10 kb | 481,132 |
1.8 Gb |
11,378 |
34.7 Mb |
|
| 10 kb - 100 kb | 48,189 |
704.9 Mb |
3,810 |
127.8 Mb |
|
| 100 kb - 1 Mb | 12 |
1.5 Mb |
2,106 |
804.6 Mb |
|
| 1 Mb - 10 Mb | 800 |
1.6 Gb |
|||