Human vs Spotted gar LastZ results

Human (Homo sapiens, GRCh38) and Spotted gar (Lepisosteus oculatus, LepOcu1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 76. 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

ParameterHumanSpotted gar
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 223,712 alignment blocks

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

Uncovered: 3,054,492,271 out of 3,096,649,726
Covered: 42,157,455 out of 3,096,649,726

Uncovered: 12,190,847 out of 35,228,305
Matches: 16,159,129 out of 35,228,305
Mismatches: 6,518,522 out of 35,228,305
Insertions: 359,807 out of 35,228,305
Identity over aligned base-pairs: 70.1%

Spotted gar

Uncovered: 914,160,653 out of 945,878,036
Covered: 31,717,383 out of 945,878,036

Uncovered: 11,608,448 out of 31,448,193
Matches: 13,961,899 out of 31,448,193
Mismatches: 5,576,488 out of 31,448,193
Insertions: 301,358 out of 31,448,193
Identity over aligned base-pairs: 70.4%

Block size distribution

Size range All 223,712 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
752
3.4 kb
10 bp - 100 bp
40,414
3.1 Mb
12,872
968.3 kb
100 bp - 1 kb
180,819
39.2 Mb
77,092
23.6 Mb
1 kb - 10 kb
2,366
3.6 Mb
8,993
18.6 Mb
10 kb - 100 kb
3
42.4 kb
155
2.4 Mb
100 kb - 1 Mb
1
124.9 kb