Zea mays vs Brachypodium distachyon LastZ Results

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Zea mays (Zea mays, B73_RefGen_v4) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Zea mays 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.

Results

Number of alignment blocks: 192,674

Genome coverage (bp) Coding exon coverage (bp)
Zea mays

Uncovered: 2,063,487,735 out of 2,135,083,061
Covered: 71,595,326 out of 2,135,083,061

Uncovered: 16,220,792 out of 48,442,923
Matches: 25,000,485 out of 48,442,923
Mismatches: 6,366,945 out of 48,442,923
Insertions: 854,701 out of 48,442,923

Brachypodium distachyon

Uncovered: 212,442,663 out of 271,163,419
Covered: 58,720,756 out of 271,163,419

Uncovered: 8,361,328 out of 39,007,317
Matches: 23,340,855 out of 39,007,317
Mismatches: 6,506,651 out of 39,007,317
Insertions: 798,483 out of 39,007,317

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Zea mays Brachypodium distachyon
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}