Arabidopsis thaliana vs Marchantia polymorpha LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Marchantia polymorpha (Marchantia polymorpha str. Tak-1, Marchanta_polymorpha_v1) 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: 68,816

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

Uncovered: 104,497,256 out of 119,667,750
Covered: 15,170,494 out of 119,667,750

Uncovered: 21,845,918 out of 33,775,569
Matches: 7,595,808 out of 33,775,569
Mismatches: 4,147,250 out of 33,775,569
Insertions: 186,593 out of 33,775,569

Marchantia polymorpha str. Tak-1

Uncovered: 214,832,521 out of 225,760,816
Covered: 10,928,295 out of 225,760,816

Uncovered: 15,857,889 out of 23,498,831
Matches: 4,852,043 out of 23,498,831
Mismatches: 2,607,762 out of 23,498,831
Insertions: 181,137 out of 23,498,831

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 Marchantia polymorpha
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}