Arabidopsis thaliana vs Aegilops tauschii LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) 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: 155,717

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

Uncovered: 92,972,330 out of 119,667,750
Covered: 26,695,420 out of 119,667,750

Uncovered: 14,152,899 out of 33,775,569
Matches: 12,557,192 out of 33,775,569
Mismatches: 6,660,650 out of 33,775,569
Insertions: 404,828 out of 33,775,569

Aegilops tauschii subsp. strangulata

Uncovered: 4,180,237,993 out of 4,224,915,394
Covered: 44,677,401 out of 4,224,915,394

Uncovered: 28,027,899 out of 53,210,770
Matches: 15,976,130 out of 53,210,770
Mismatches: 8,482,045 out of 53,210,770
Insertions: 724,696 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

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}