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Human vs Duck LastZ alignments

Human (Homo sapiens, GRCh37) and Duck (Anas platyrhynchos, BGI_duck_1.0) 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 Duck
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: 303,276

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

Uncovered: 3,017,123,226 out of 3,098,825,702
Covered: 81,702,476 out of 3,098,825,702

Uncovered: 10,235,179 out of 35,266,550
Matches: 18,506,038 out of 35,266,550
Mismatches: 6,238,608 out of 35,266,550
Insertions: 286,725 out of 35,266,550

Anas platyrhynchos

Uncovered: 1,036,918,192 out of 1,105,035,747
Covered: 68,117,555 out of 1,105,035,747

Uncovered: 3,060,074 out of 23,616,868
Matches: 15,418,171 out of 23,616,868
Mismatches: 4,934,644 out of 23,616,868
Insertions: 203,979 out of 23,616,868