Arabidopsis thaliana vs Aegilops tauschii LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Aegilops tauschii (Aegilops tauschii, ASM34733v1) 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: 143,189

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

Uncovered: 92,896,761 out of 119,667,750
Covered: 26,770,989 out of 119,667,750

Uncovered: 14,531,718 out of 33,775,569
Matches: 12,052,128 out of 33,775,569
Mismatches: 6,811,436 out of 33,775,569
Insertions: 380,287 out of 33,775,569

Aegilops tauschii

Uncovered: 3,275,180,047 out of 3,313,764,331
Covered: 38,584,284 out of 3,313,764,331

Uncovered: 21,684,582 out of 40,847,881
Matches: 12,230,977 out of 40,847,881
Mismatches: 6,480,863 out of 40,847,881
Insertions: 451,459 out of 40,847,881

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 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}