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Triticum aestivum vs Brachypodium distachyon LastZ Results

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Triticum aestivum (Triticum aestivum, IWGSC) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Triticum aestivum 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.


Number of alignment blocks: 2,227,317

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 13,651,982,362 out of 14,547,261,565
Covered: 895,279,203 out of 14,547,261,565

Uncovered: 8,433,093 out of 136,655,258
Matches: 103,740,468 out of 136,655,258
Mismatches: 21,833,860 out of 136,655,258
Insertions: 2,647,837 out of 136,655,258

Brachypodium distachyon

Uncovered: 145,247,128 out of 271,163,419
Covered: 125,916,291 out of 271,163,419

Uncovered: 2,592,219 out of 39,007,317
Matches: 29,466,875 out of 39,007,317
Mismatches: 6,028,796 out of 39,007,317
Insertions: 919,427 out of 39,007,317

Configuration parameters

Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
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)
     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

Triticum aestivum Brachypodium distachyon
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}