Brachypodium distachyon vs Aegilops tauschii LastZ Results

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Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) 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: 801,048

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

Uncovered: 155,031,446 out of 271,163,419
Covered: 116,131,973 out of 271,163,419

Uncovered: 2,992,705 out of 39,007,317
Matches: 29,194,870 out of 39,007,317
Mismatches: 5,948,692 out of 39,007,317
Insertions: 871,050 out of 39,007,317

Aegilops tauschii subsp. strangulata

Uncovered: 3,928,206,844 out of 4,224,915,394
Covered: 296,708,550 out of 4,224,915,394

Uncovered: 5,013,787 out of 53,210,770
Matches: 38,486,786 out of 53,210,770
Mismatches: 8,435,615 out of 53,210,770
Insertions: 1,274,582 out of 53,210,770

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 Aegilops tauschii
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}