Arabidopsis thaliana vs Amborella trichopoda LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Amborella trichopoda (Amborella trichopoda, AMTR1.0) 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: 116,386

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

Uncovered: 93,320,892 out of 119,667,750
Covered: 26,346,858 out of 119,667,750

Uncovered: 13,496,593 out of 33,775,569
Matches: 13,325,467 out of 33,775,569
Mismatches: 6,561,294 out of 33,775,569
Insertions: 392,215 out of 33,775,569

Amborella trichopoda

Uncovered: 682,248,663 out of 706,332,640
Covered: 24,083,977 out of 706,332,640

Uncovered: 10,370,882 out of 25,807,211
Matches: 10,109,768 out of 25,807,211
Mismatches: 4,957,944 out of 25,807,211
Insertions: 368,617 out of 25,807,211

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 Amborella trichopoda
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}