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Human vs Armadillo LastZ alignments

Human (Homo sapiens, GRCh37) and Armadillo (Dasypus novemcinctus, Dasnov3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 74. Human was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is 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

Human Armadillo
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}

Results

Number of alignment blocks: 1,798,016

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 1,710,521,261 out of 3,098,825,702
Covered: 1,388,304,441 out of 3,098,825,702

Uncovered: 1,665,544 out of 35,274,750
Matches: 28,825,580 out of 35,274,750
Mismatches: 4,440,268 out of 35,274,750
Insertions: 343,358 out of 35,274,750

Dasypus novemcinctus

Uncovered: 2,329,350,213 out of 3,631,522,711
Covered: 1,302,172,498 out of 3,631,522,711

Uncovered: 4,938,788 out of 34,329,446
Matches: 25,548,079 out of 34,329,446
Mismatches: 3,663,913 out of 34,329,446
Insertions: 178,666 out of 34,329,446