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Human vs Spotted gar LastZ alignments

Human (Homo sapiens, GRCh37) and Spotted gar (Lepisosteus oculatus, LepOcu1) 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 Spotted gar
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: 232,763

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

Uncovered: 3,056,273,565 out of 3,098,825,702
Covered: 42,552,137 out of 3,098,825,702

Uncovered: 12,275,284 out of 35,274,750
Matches: 16,123,715 out of 35,274,750
Mismatches: 6,510,068 out of 35,274,750
Insertions: 365,683 out of 35,274,750

Lepisosteus oculatus

Uncovered: 912,891,879 out of 945,878,036
Covered: 32,986,157 out of 945,878,036

Uncovered: 11,051,780 out of 31,448,193
Matches: 14,363,151 out of 31,448,193
Mismatches: 5,723,829 out of 31,448,193
Insertions: 309,433 out of 31,448,193