Human vs Upper Galilee mountains blind mole rat LastZ results
Human (Homo sapiens, GRCh38) and Upper Galilee mountains blind mole rat (Nannospalax galili, S.galili_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 90. 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 |
| Masking count (M) | |
| 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 | Upper Galilee mountains blind mole rat |
|---|---|---|
| Chunk size | 10,000,000 | 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 2,069,260 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 1,834,156,083 out of 3,096,649,726 |
Uncovered: 1,007,105 out of 35,444,608 |
| Upper Galilee mountains blind mole rat |
Uncovered: 1,905,047,514 out of 3,061,408,210 |
Uncovered: 1,146,175 out of 29,132,429 |
Block size distribution
| Size range | All 2,069,260 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 48,088 |
321.9 kb |
|||
| 10 bp - 100 bp | 232,429 |
12.0 Mb |
15,003 |
1.0 Mb |
|
| 100 bp - 1 kb | 1,382,036 |
613.5 Mb |
63,421 |
23.8 Mb |
|
| 1 kb - 10 kb | 406,482 |
698.1 Mb |
19,830 |
46.8 Mb |
|
| 10 kb - 100 kb | 225 |
2.8 Mb |
1,601 |
43.7 Mb |
|
| 100 kb - 1 Mb | 848 |
353.1 Mb |
|||
| 1 Mb - 10 Mb | 398 |
858.3 Mb |
|||