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Chicken vs Duck LastZ Results

Chicken (Gallus gallus, Galgal4) and Duck (Anas platyrhynchos, BGI_duck_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 73. Chicken 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

ParameterChickenDuck
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 832,975 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Chicken

Uncovered: 199,023,352 out of 1,046,932,099
Covered: 847,908,747 out of 1,046,932,099

Uncovered: 1,632,197 out of 25,934,237
Matches: 21,816,348 out of 25,934,237
Mismatches: 2,388,802 out of 25,934,237
Insertions: 96,890 out of 25,934,237

Duck

Uncovered: 266,598,160 out of 1,105,035,747
Covered: 838,437,587 out of 1,105,035,747

Uncovered: 789,480 out of 23,616,868
Matches: 20,674,287 out of 23,616,868
Mismatches: 2,046,432 out of 23,616,868
Insertions: 106,669 out of 23,616,868