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Human vs Flycatcher LastZ alignments

Human (Homo sapiens, GRCh37) and Flycatcher (Ficedula albicollis, FicAlb_1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 73. 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 Flycatcher
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: 288,409

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

Uncovered: 3,020,797,895 out of 3,098,825,702
Covered: 78,027,807 out of 3,098,825,702

Uncovered: 9,942,745 out of 35,266,550
Matches: 18,717,205 out of 35,266,550
Mismatches: 6,273,429 out of 35,266,550
Insertions: 333,171 out of 35,266,550

Ficedula albicollis

Uncovered: 1,052,212,073 out of 1,116,409,277
Covered: 64,197,204 out of 1,116,409,277

Uncovered: 4,247,302 out of 25,179,529
Matches: 15,666,869 out of 25,179,529
Mismatches: 5,039,156 out of 25,179,529
Insertions: 226,202 out of 25,179,529