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Human vs Chacoan peccary LastZ results

Human (Homo sapiens, GRCh38) and Chacoan peccary (Catagonus wagneri, CatWag_v2_BIUU_UCD) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 99. 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
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

ParameterHumanChacoan peccary
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 2,179,370 alignment blocks

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

Uncovered: 1,639,218,851 out of 3,099,750,718
Covered: 1,460,531,867 out of 3,099,750,718

Uncovered: 1,758,213 out of 38,571,754
Matches: 31,299,741 out of 38,571,754
Mismatches: 5,050,640 out of 38,571,754
Insertions: 463,160 out of 38,571,754
Identity over aligned base-pairs: 85.0%

Chacoan peccary

Uncovered: 1,277,517,120 out of 2,640,067,814
Covered: 1,362,550,694 out of 2,640,067,814

Uncovered: 940,781 out of 31,494,020
Matches: 26,855,009 out of 31,494,020
Mismatches: 3,586,135 out of 31,494,020
Insertions: 112,095 out of 31,494,020
Identity over aligned base-pairs: 87.9%

Block size distribution

Size range All 2,179,370 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
80,021
532.1 kb
10 bp - 100 bp
266,221
13.0 Mb
18,108
1.2 Mb
100 bp - 1 kb
1,340,228
598.4 Mb
63,203
23.2 Mb
1 kb - 10 kb
492,239
913.5 Mb
18,105
43.5 Mb
10 kb - 100 kb
658
9.3 Mb
1,540
39.2 Mb
100 kb - 1 Mb
3
303.3 kb
300
96.7 Mb
1 Mb - 10 Mb
189
658.9 Mb
10 Mb - 100 Mb
38
672.3 Mb