Arabidopsis thaliana vs Brachypodium distachyon LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brachypodium distachyon (Brachypodium distachyon, v1.0) 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: 109,475

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

Uncovered: 93,550,273 out of 119,667,750
Covered: 26,117,477 out of 119,667,750

Uncovered: 14,347,966 out of 33,775,569
Matches: 12,594,073 out of 33,775,569
Mismatches: 6,443,053 out of 33,775,569
Insertions: 390,477 out of 33,775,569

Brachypodium distachyon

Uncovered: 244,416,951 out of 271,923,306
Covered: 27,506,355 out of 271,923,306

Uncovered: 14,931,882 out of 34,177,820
Matches: 12,380,531 out of 34,177,820
Mismatches: 6,398,547 out of 34,177,820
Insertions: 466,860 out of 34,177,820

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

Arabidopsis thaliana 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}