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Human vs Microbat LastZ alignments

Human (Homo sapiens, GRCh37) and Microbat (Myotis lucifugus, Myoluc2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 63. 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)2200
Threshold for alignments between gapped alignment blocks (H)2000
Masking count (M)50
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 Microbat
Chunk size 10,000,000 10,010,000
Overlap 0 10,000
Group set size 0 10,010,000
Masking options {default_soft_masking => 1}

Results

Number of alignment blocks: 1,815,112

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

Uncovered: 1,898,493,509 out of 3,098,825,702
Covered: 1,200,332,193 out of 3,098,825,702

Uncovered: 2,753,560 out of 35,313,516
Matches: 27,811,510 out of 35,313,516
Mismatches: 4,404,453 out of 35,313,516
Insertions: 343,993 out of 35,313,516

Myotis lucifugus

Uncovered: 917,520,915 out of 2,034,575,300
Covered: 1,117,054,385 out of 2,034,575,300

Uncovered: 2,968,180 out of 30,512,546
Matches: 24,097,417 out of 30,512,546
Mismatches: 3,313,968 out of 30,512,546
Insertions: 132,981 out of 30,512,546