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Anole lizard vs Chinese softshell turtle LastZ alignments

Anole lizard (Anolis carolinensis, AnoCar2.0) and Chinese softshell turtle (Pelodiscus sinensis, PelSin_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 68. Anole lizard 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)
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

Anole lizard Chinese softshell turtle
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}

Results

Number of alignment blocks: 721,612

Genome coverage (bp) Coding exon coverage (bp)
Anolis carolinensis

Uncovered: 1,602,487,936 out of 1,799,143,587
Covered: 196,655,651 out of 1,799,143,587

Uncovered: 3,681,578 out of 27,370,256
Matches: 18,158,178 out of 27,370,256
Mismatches: 5,306,691 out of 27,370,256
Insertions: 223,809 out of 27,370,256

Pelodiscus sinensis

Uncovered: 2,102,735,073 out of 2,202,483,752
Covered: 99,748,679 out of 2,202,483,752

Uncovered: 7,079,915 out of 28,388,868
Matches: 16,494,001 out of 28,388,868
Mismatches: 4,606,828 out of 28,388,868
Insertions: 208,124 out of 28,388,868