Arabidopsis thaliana vs Brachypodium distachyon LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 108,532

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,675,392 out of 119,667,750
Covered: 25,992,358 out of 119,667,750

Uncovered: 14,393,303 out of 33,775,569
Matches: 12,552,135 out of 33,775,569
Mismatches: 6,440,411 out of 33,775,569
Insertions: 389,720 out of 33,775,569

Brachypodium distachyon

Uncovered: 243,913,132 out of 271,163,419
Covered: 27,250,287 out of 271,163,419

Uncovered: 19,297,885 out of 39,007,317
Matches: 12,658,688 out of 39,007,317
Mismatches: 6,570,724 out of 39,007,317
Insertions: 480,020 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

Arabidopsis thaliana 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}