Brachypodium distachyon vs Triticum turgidum LastZ Results

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Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) and Triticum turgidum (Triticum turgidum, Svevo.v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Brachypodium distachyon 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: 1,747,583

Genome coverage (bp) Coding exon coverage (bp)
Brachypodium distachyon

Uncovered: 148,077,163 out of 271,163,419
Covered: 123,086,256 out of 271,163,419

Uncovered: 2,695,527 out of 39,007,317
Matches: 29,374,172 out of 39,007,317
Mismatches: 6,029,515 out of 39,007,317
Insertions: 908,103 out of 39,007,317

Triticum turgidum

Uncovered: 9,789,027,155 out of 10,463,058,104
Covered: 674,030,949 out of 10,463,058,104

Uncovered: 5,622,236 out of 88,577,667
Matches: 67,097,581 out of 88,577,667
Mismatches: 14,097,550 out of 88,577,667
Insertions: 1,760,300 out of 88,577,667

Configuration parameters

ParameterValue
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)
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

Brachypodium distachyon Triticum turgidum
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}