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Chicken vs Zebra Finch LastZ Results

Chicken (Gallus gallus, Galgal4) and Zebra Finch (Taeniopygia guttata, taeGut3.2.4) 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)50
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

ParameterChickenZebra Finch
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 815,468 alignment blocks

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

Uncovered: 294,921,805 out of 1,046,932,099
Covered: 752,010,294 out of 1,046,932,099

Uncovered: 1,707,889 out of 25,934,237
Matches: 20,810,574 out of 25,934,237
Mismatches: 3,245,599 out of 25,934,237
Insertions: 170,175 out of 25,934,237

Zebra Finch

Uncovered: 499,219,144 out of 1,233,186,341
Covered: 733,967,197 out of 1,233,186,341

Uncovered: 2,575,396 out of 23,643,636
Matches: 18,445,003 out of 23,643,636
Mismatches: 2,542,393 out of 23,643,636
Insertions: 80,844 out of 23,643,636