Brachypodium distachyon vs Triticum dicoccoides LastZ Results

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Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) and Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) 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: 932,208

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

Uncovered: 154,569,800 out of 271,163,419
Covered: 116,593,619 out of 271,163,419

Uncovered: 2,928,706 out of 39,007,317
Matches: 29,336,751 out of 39,007,317
Mismatches: 5,847,443 out of 39,007,317
Insertions: 894,417 out of 39,007,317

Triticum dicoccoides

Uncovered: 9,657,511,005 out of 10,079,039,394
Covered: 421,528,389 out of 10,079,039,394

Uncovered: 5,052,599 out of 81,268,905
Matches: 62,507,456 out of 81,268,905
Mismatches: 12,130,613 out of 81,268,905
Insertions: 1,578,237 out of 81,268,905

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 dicoccoides
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}