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Human vs Chicken LastZ alignments

Human (Homo sapiens, GRCh37) and Chicken (Gallus gallus, Galgal4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 71. 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 Chicken
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: 320,266

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

Uncovered: 3,015,955,152 out of 3,098,825,702
Covered: 82,870,550 out of 3,098,825,702

Uncovered: 9,163,081 out of 35,270,662
Matches: 19,218,213 out of 35,270,662
Mismatches: 6,523,840 out of 35,270,662
Insertions: 365,528 out of 35,270,662

Gallus gallus

Uncovered: 978,706,946 out of 1,046,932,099
Covered: 68,225,153 out of 1,046,932,099

Uncovered: 4,032,189 out of 25,934,237
Matches: 16,340,817 out of 25,934,237
Mismatches: 5,317,530 out of 25,934,237
Insertions: 243,701 out of 25,934,237