Human vs Squirrel LastZ results

Human (Homo sapiens, GRCh38) and Squirrel (Ictidomys tridecemlineatus, SpeTri2.0) 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

ParameterValue
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

ParameterHumanSquirrel
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 2,151,857 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Human

Uncovered: 1,566,630,535 out of 3,096,649,726
Covered: 1,530,019,191 out of 3,096,649,726

Uncovered: 1,259,281 out of 35,387,657
Matches: 29,594,978 out of 35,387,657
Mismatches: 4,237,695 out of 35,387,657
Insertions: 295,703 out of 35,387,657
Identity over aligned base-pairs: 86.7%

Squirrel

Uncovered: 1,064,187,966 out of 2,478,410,228
Covered: 1,414,222,262 out of 2,478,410,228

Uncovered: 0 out of 11,330
Matches: 8,037 out of 11,330
Mismatches: 3,262 out of 11,330
Insertions: 31 out of 11,330
Identity over aligned base-pairs: 70.9%

Block size distribution

Size range All 2,151,857 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
67,677
453.9 kb
10 bp - 100 bp
267,513
13.0 Mb
17,862
1.2 Mb
100 bp - 1 kb
1,291,281
574.9 Mb
62,986
21.9 Mb
1 kb - 10 kb
524,771
1.0 Gb
18,948
46.4 Mb
10 kb - 100 kb
615
7.8 Mb
1,689
41.1 Mb
100 kb - 1 Mb
301
112.9 Mb
1 Mb - 10 Mb
318
1.0 Gb
10 Mb - 100 Mb
22
357.7 Mb