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Chicken vs Turkey LastZ Results

Chicken (Gallus gallus, Galgal4) and Turkey (Meleagris gallopavo, UMD2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 71. 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

ParameterChickenTurkey
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 381,029 alignment blocks

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

Uncovered: 118,266,026 out of 1,046,932,099
Covered: 928,666,073 out of 1,046,932,099

Uncovered: 1,463,487 out of 25,934,237
Matches: 23,312,788 out of 25,934,237
Mismatches: 1,104,154 out of 25,934,237
Insertions: 53,808 out of 25,934,237

Turkey

Uncovered: 174,594,894 out of 1,061,998,909
Covered: 887,404,015 out of 1,061,998,909

Uncovered: 187,215 out of 22,798,877
Matches: 21,734,610 out of 22,798,877
Mismatches: 849,943 out of 22,798,877
Insertions: 27,109 out of 22,798,877